macでインフォマティクス

macでインフォマティクス

NGS関連のインフォマティクス情報についてまとめています。

Nanoporeのオフィシャルコマンドラインbasecaller2 Guppy(GPU対応版もあり)

 2019 3/12 タイトル修正

2019 3/12 コマンド追記、誤ったコメント削除

 

GuppyはOxford Nanoporeによって提供されているコマンドラインのbasecaller。 そしてポアを通過するDNAまたはRNAをbasecallingするために最新のリカレントニューラルネットワークアルゴリズムを利用してナノポアからのシグナルデータを解釈する。GPU GuppyはOxford Nanopore Technologiesのソフトウェア製品に安定した機能を実装しており、完全にサポートされている。 .fast5ファイルを入力として受け取り、ベースコール情報を付加した.fast5ファイル、処理された.fast5ファイル(1D^2は2回ランする)、fastqファイルを生成できる。

 

マニュアルリンク

Log in - Oxford Nanopore Technologies

f:id:kazumaxneo:20190310134908j:plain

log inの必要あり。

 

インストール

mac10.12でバイナリをダウンロードしてテストした。

ハードウエア要件

  • 4 GBのRAMと1 Dベースコールのスレッドあたり1 GB
  • 4 GBのRAMと1 D 2ベースコールのスレッドあたり2 GB
  • .debまたは.msiインストーラーの管理者アクセス
  • インストール用に最大100 MBのドライブスペース、ベースコールされたリードファイル用に最低512 GBのストレージスペース(1 TB推奨)
  • 外部GPUGPU版)

Albacoreと同様、ダウンロードはOxford nanopore HPのsoftware downloadsから行う。

f:id:kazumaxneo:20190310124044j:plain

バイナリがダウンロードできる。ここではmac os向けバイナリをダウンロードした。gpu版のバイナリはcentos7版のみ用意されている。

cd ont-guppy-cpu/bin/

> ls -l

$ ls -l

total 18360

-rw-r--r--@ 1 user  staff   196187 12 11 15:37 Nanopore Community TCs 09 September 2016.pdf

-rw-r--r--@ 1 user  staff    57178  1 28 17:16 THIRD_PARTY_LICENSES

-rwxr-xr-x@ 1 user  staff   950944  2 26 14:22 guppy_aligner

-rwxr-xr-x@ 1 user  staff  1098576  2 26 14:22 guppy_barcoder

-rwxr-xr-x@ 1 user  staff  1774404  2 26 14:22 guppy_basecall_server

-rwxr-xr-x@ 1 user  staff  2707612  2 26 14:22 guppy_basecaller

-rwxr-xr-x@ 1 user  staff  2598784  2 26 14:22 guppy_basecaller_1d2

./guppy_basecaller

$ ./guppy_basecaller

: Guppy Basecalling Software, (C) Oxford Nanopore Technologies, Limited. Version 2.3.5+53a111f6

 

Usage:

 

With config file:

  guppy_basecaller -i <input path> -s <save path> -c <config file> [options]

With flowcell and kit name:

  guppy_basecaller -i <input path> -s <save path> --flowcell <flowcell name>

    --kit <kit name>

List supported flowcells and kits:

  guppy_basecaller --print_workflows

Use server for basecalling:

  guppy_basecaller -i <input path> -s <save path> -c <config file>

    --port <server address> [options] 

 

Command line parameters:

  --print_workflows                 Output available workflows.

  --flowcell arg                    Flowcell to find a configuration for

  --kit arg                         Kit to find a configuration for

  -m [ --model_file ] arg           Path to JSON model file.

  --chunk_size arg                  Stride intervals per chunk.

  --chunks_per_runner arg           Maximum chunks per runner.

  --chunks_per_caller arg           Soft limit on number of chunks in each 

                                    caller's queue. New reads will not be 

                                    queued while this is exceeded.

  --overlap arg                     Overlap between chunks (in stride 

                                    intervals).

  --gpu_runners_per_device arg      Number of runners per GPU device.

  --cpu_threads_per_caller arg      Number of CPU worker threads per 

                                    basecaller.

  --num_callers arg                 Number of parallel basecallers to create.

  --stay_penalty arg                Scaling factor to apply to stay probability

                                    calculation during transducer decode.

  --qscore_offset arg               Qscore calibration offset.

  --qscore_scale arg                Qscore calibration scale factor.

  --temp_weight arg                 Temperature adjustment for weight matrix in

                                    softmax layer of RNN.

  --temp_bias arg                   Temperature adjustment for bias vector in 

                                    softmax layer of RNN.

  --hp_correct arg                  Whether to use homopolymer correction 

                                    during decoding.

  --builtin_scripts arg             Whether to use GPU kernels that were 

                                    included at compile-time.

  -x [ --device ] arg               Specify basecalling device: 'auto', or 

                                    'cuda:<device_id>'.

  -k [ --kernel_path ] arg          Path to GPU kernel files location (only 

                                    needed if builtin_scripts is false).

  -z [ --quiet ]                    Quiet mode. Nothing will be output to 

                                    STDOUT if this option is set.

  --trace_categories_logs arg       Enable trace logs - list of strings with 

                                    the desired names.

  --verbose_logs                    Enable verbose logs.

  --qscore_filtering                Enable filtering of reads into PASS/FAIL 

                                    folders based on min qscore.

  --min_qscore arg                  Minimum acceptable qscore for a read to be 

                                    filtered into the PASS folder

  --disable_pings                   Disable the transmission of telemetry 

                                    pings.

  --ping_url arg                    URL to send pings to

  --ping_segment_duration arg       Duration in minutes of each ping segment.

  --calib_detect                    Enable calibration strand detection and 

                                    filtering.

  --calib_reference arg             Reference FASTA file containing calibration

                                    strand.

  --calib_min_sequence_length arg   Minimum sequence length for reads to be 

                                    considered candidate calibration strands.

  --calib_max_sequence_length arg   Maximum sequence length for reads to be 

                                    considered candidate calibration strands.

  --calib_min_coverage arg          Minimum reference coverage to pass 

                                    calibration strand detection.

  -q [ --records_per_fastq ] arg    Maximum number of records per fastq file, 0

                                    means use a single file (per worker, per 

                                    run id).

  --enable_trimming arg             Enable adapter trimming.

  --trim_threshold arg              Threshold above which data will be trimmed 

                                    (in standard deviations of current level 

                                    distribution).

  --trim_min_events arg             Adapter trimmer minimum stride intervals 

                                    after stall that must be seen.

  --max_search_len arg              Maximum number of samples to search through

                                    for the stall

  --reverse_sequence arg            Reverse the called sequence (for RNA 

                                    sequencing).

  --u_substitution arg              Substitute 'U' for 'T' in the called 

                                    sequence (for RNA sequencing).

  -i [ --input_path ] arg           Path to input fast5 files.

  -s [ --save_path ] arg            Path to save fastq files.

  -l [ --read_id_list ] arg         File containing list of read ids to filter 

                                    to

  -p [ --port ] arg                 Hostname and port for connecting to 

                                    basecall service (ie 'myserver:5555'), or 

                                    port only (ie '5555'), in which case 

                                    localhost is assumed.

  -r [ --recursive ]                Search for input files recursively.

  --fast5_out                       Choice of whether to do fast5 output.

  --override_scaling                Manually provide scaling parameters rather 

                                    than estimating them from each read.

  --scaling_med arg                 Median current value to use for manual 

                                    scaling.

  --scaling_mad arg                 Median absolute deviation to use for manual

                                    scaling.

  --trim_strategy arg               Trimming strategy to apply ('dna' or 'rna')

  --dmean_win_size arg              Window size for coarse stall event 

                                    detection

  --dmean_threshold arg             Threhold for coarse stall event detection

  --jump_threshold arg              Threshold level for rna stall detection

  --disable_events                  Disable the transmission of event tables 

                                    when receiving reads back from the basecall

                                    server.

  --pt_scaling                      Enable polyT/adapter max detection for read

                                    scaling.

  --pt_median_offset arg            Set polyT median offset for setting read 

                                    scaling median (default 2.5)

  --adapter_pt_range_scale arg      Set polyT/adapter range scale for setting 

                                    read scaling median absolute deviation 

                                    (default 5.2)

  --pt_required_adapter_drop arg    Set minimum required current drop from 

                                    adapter max to polyT detection. (default 

                                    30.0)

  --pt_minimum_read_start_index arg Set minimum index for read start sample 

                                    required to attempt polyT scaling. (default

                                    30)

  -h [ --help ]                     produce help message

  -v [ --version ]                  print version number

  -c [ --config ] arg               Config file to use

  -d [ --data_path ] arg            Path to use for loading any data files the 

                                    application requires.

 

./guppy_basecaller_1d2

$ ./guppy_basecaller_1d2

: Guppy 1D-Squared Basecalling Software, (C) Oxford Nanopore Technologies, Limited. Version 2.3.5+53a111f6

Command line parameters:

  --print_workflows               Output available workflows.

  --flowcell arg                  Flowcell to find a configuration for

  --kit arg                       Kit to find a configuration for

  -m [ --model_file ] arg         Path to JSON model file.

  --chunk_size arg                Stride intervals per chunk.

  --chunks_per_runner arg         Maximum chunks per runner.

  --chunks_per_caller arg         Soft limit on number of chunks in each 

                                  caller's queue. New reads will not be queued 

                                  while this is exceeded.

  --overlap arg                   Overlap between chunks (in stride intervals).

  --gpu_runners_per_device arg    Number of runners per GPU device.

  --cpu_threads_per_caller arg    Number of CPU worker threads per basecaller.

  --num_callers arg               Number of parallel basecallers to create.

  --stay_penalty arg              Scaling factor to apply to stay probability 

                                  calculation during transducer decode.

  --qscore_offset arg             Qscore calibration offset.

  --qscore_scale arg              Qscore calibration scale factor.

  --temp_weight arg               Temperature adjustment for weight matrix in 

                                  softmax layer of RNN.

  --temp_bias arg                 Temperature adjustment for bias vector in 

                                  softmax layer of RNN.

  --hp_correct arg                Whether to use homopolymer correction during 

                                  decoding.

  --builtin_scripts arg           Whether to use GPU kernels that were included

                                  at compile-time.

  -x [ --device ] arg             Specify basecalling device: 'auto', or 

                                  'cuda:<device_id>'.

  -k [ --kernel_path ] arg        Path to GPU kernel files location (only 

                                  needed if builtin_scripts is false).

  -z [ --quiet ]                  Quiet mode. Nothing will be output to STDOUT 

                                  if this option is set.

  --trace_categories_logs arg     Enable trace logs - list of strings with the 

                                  desired names.

  --verbose_logs                  Enable verbose logs.

  --qscore_filtering              Enable filtering of reads into PASS/FAIL 

                                  folders based on min qscore.

  --min_qscore arg                Minimum acceptable qscore for a read to be 

                                  filtered into the PASS folder

  --disable_pings                 Disable the transmission of telemetry pings.

  --ping_url arg                  URL to send pings to

  --ping_segment_duration arg     Duration in minutes of each ping segment.

  --calib_detect                  Enable calibration strand detection and 

                                  filtering.

  --calib_reference arg           Reference FASTA file containing calibration 

                                  strand.

  --calib_min_sequence_length arg Minimum sequence length for reads to be 

                                  considered candidate calibration strands.

  --calib_max_sequence_length arg Maximum sequence length for reads to be 

                                  considered candidate calibration strands.

  --calib_min_coverage arg        Minimum reference coverage to pass 

                                  calibration strand detection.

  --score_matrix arg              Path to mismatch matrix for prior label 

                                  alignment

  -q [ --records_per_fastq ] arg  Maximum number of records per fastq file (0 

                                  means use a single file).

  --winsize1 arg                  Short window length for event detection.

  --winsize2 arg                  Long window length for event detection.

  --threshold1 arg                Shirt time-scale threshold for event 

                                  detection.

  --threshold2 arg                Long time-scale threshold for event 

                                  detection.

  --band_size arg                 Band size for 1d-squared alignment table.

  --pa_band_size arg              Band size for prior-alignment table.

  --gap_penalty arg               Gap penalty for prior label alignment.

  --start_end_penalty arg         Overhang penalty for prior label alignment.

  --reverse_sequence arg          Reverse the called sequence (for RNA 

                                  sequencing).

  --u_substitution arg            Substute 'U' for 'T' in the called sequence 

                                  (for RNA sequencing).

  -i [ --input_path ] arg         Path to input fast5 files.

  -f [ --index_file ] arg         Index file from 1D basecall.

  -s [ --save_path ] arg          Path to save fastq files.

  -p [ --port ] arg               Hostname and port for connecting to basecall 

                                  service (ie 'myserver:5555'), or port only 

                                  (ie '5555'), in which case localhost is 

                                  assumed.

  -r [ --recursive ]              Search for input files recursively.

  --override_scaling              Manually provide scaling parameters rather 

                                  than estimating them from each read.

  --scaling_med arg               Median current value to use for manual 

                                  scaling.

  --scaling_mad arg               Median absolute deviation to use for manual 

                                  scaling.

  -h [ --help ]                   produce help message

  -v [ --version ]                print version number

  -c [ --config ] arg             Config file to use

  -d [ --data_path ] arg          Path to use for loading any data files the 

                                  application requires.

 

./guppy_barcoder 

$ ./guppy_barcoder 

 

Usage:

 

  guppy_barcoder -i <input fastq path> -s <save path>

With kit name:

  guppy_barcoder -i <input fastq path> -s <save path> --barcode_kits <kit name>

    --kit <kit name>

List supported barcoding kits:

  guppy_barcoder --print_kits

 

Command line parameters:

  -z [ --quiet ]                 Quiet mode. Nothing will be output to stdout 

                                 if this option is set.

  -t [ --worker_threads ] arg    Number of worker threads.

  -i [ --input_path ] arg        Path to input fastq files.

  -s [ --save_path ] arg         Path to save fastq files.

  -r [ --recursive ]             Search for input file recursively.

  --trace_categories_logs arg    Enable trace logs - list of strings with the 

                                 desired names.

  --verbose_logs                 Enable verbose logs.

  --print_kits                   Output all available barcoding kits.

  --barcode_kits arg             Space separated list of barcoding kit(s) or 

                                 expansion kit(s) to detect against. Must be in

                                 double quotes.

  -q [ --records_per_fastq ] arg Maximum number of records per fastq file, 0 

                                 means use a single file (per run id).

  --arrangements_files arg       Files containing arrangements.

  --score_matrix_filename arg    File containing mismatch score matrix.

  --start_gap1 arg               Gap penalty for aligning before the reference.

  --end_gap1 arg                 Gap penalty for aligning after the reference.

  --open_gap1 arg                Penalty for opening a new gap in the 

                                 reference.

  --extend_gap1 arg              Penalty for extending a gap in the reference.

  --start_gap2 arg               Gap penalty for aligning before the query.

  --end_gap2 arg                 Gap penalty for aligning after the query.

  --open_gap2 arg                Penalty for opening a new gap in the query.

  --extend_gap2 arg              Penalty for extending a gap in the query.

  --min_score arg                Minimum score to consider a valid alignment.

  --front_window_size arg        Window size for the beginning barcode.

  --rear_window_size arg         Window size for the ending barcode.

  -h [ --help ]                  produce help message

  -v [ --version ]               print version number

  -c [ --config ] arg            Config file to use

  -d [ --data_path ] arg         Path to use for loading any data files the 

                                 application requires.

./guppy_basecall_server

$ ./guppy_basecall_server

: Guppy Basecall Service Software, (C) Oxford Nanopore Technologies, Limited. Version 2.3.5+53a111f6

 

Usage:

 

With config file:

  guppy_basecall_server -c <config file> --port <server listen port>

    --log_path <log file path> [options]

With flowcell and kit:

  guppy_basecall_server --flowcell <flowcell name> --kit <kit name>

    --port <server listen port> --log_path <log file path> [options]

List supported flowcells and kits:

  guppy_basecall_server --print_workflows

 

Command line parameters:

  --print_workflows               Output available workflows.

  --flowcell arg                  Flowcell to find a configuration for

  --kit arg                       Kit to find a configuration for

  -m [ --model_file ] arg         Path to JSON model file.

  --chunk_size arg                Stride intervals per chunk.

  --chunks_per_runner arg         Maximum chunks per runner.

  --chunks_per_caller arg         Soft limit on number of chunks in each 

                                  caller's queue. New reads will not be queued 

                                  while this is exceeded.

  --overlap arg                   Overlap between chunks (in stride intervals).

  --gpu_runners_per_device arg    Number of runners per GPU device.

  --cpu_threads_per_caller arg    Number of CPU worker threads per basecaller.

  --num_callers arg               Number of parallel basecallers to create.

  --stay_penalty arg              Scaling factor to apply to stay probability 

                                  calculation during transducer decode.

  --qscore_offset arg             Qscore calibration offset.

  --qscore_scale arg              Qscore calibration scale factor.

  --temp_weight arg               Temperature adjustment for weight matrix in 

                                  softmax layer of RNN.

  --temp_bias arg                 Temperature adjustment for bias vector in 

                                  softmax layer of RNN.

  --hp_correct arg                Whether to use homopolymer correction during 

                                  decoding.

  --builtin_scripts arg           Whether to use GPU kernels that were included

                                  at compile-time.

  -x [ --device ] arg             Specify basecalling device: 'auto', or 

                                  'cuda:<device_id>'.

  -k [ --kernel_path ] arg        Path to GPU kernel files location (only 

                                  needed if builtin_scripts is false).

  -z [ --quiet ]                  Quiet mode. Nothing will be output to STDOUT 

                                  if this option is set.

  --trace_categories_logs arg     Enable trace logs - list of strings with the 

                                  desired names.

  --verbose_logs                  Enable verbose logs.

  --qscore_filtering              Enable filtering of reads into PASS/FAIL 

                                  folders based on min qscore.

  --min_qscore arg                Minimum acceptable qscore for a read to be 

                                  filtered into the PASS folder

  --disable_pings                 Disable the transmission of telemetry pings.

  --ping_url arg                  URL to send pings to

  --ping_segment_duration arg     Duration in minutes of each ping segment.

  --calib_detect                  Enable calibration strand detection and 

                                  filtering.

  --calib_reference arg           Reference FASTA file containing calibration 

                                  strand.

  --calib_min_sequence_length arg Minimum sequence length for reads to be 

                                  considered candidate calibration strands.

  --calib_max_sequence_length arg Maximum sequence length for reads to be 

                                  considered candidate calibration strands.

  --calib_min_coverage arg        Minimum reference coverage to pass 

                                  calibration strand detection.

  --ipc_threads arg               Number of threads to use for inter-process 

                                  communication.

  --max_queued_reads arg          Maximum number of reads in input queue.

  -l [ --log_path ] arg           Path to save log file.

  -p [ --port ] arg               Port for hosting service. Specify "auto" to 

                                  make server automatically search for a free 

                                  port.

  -h [ --help ]                   produce help message

  -v [ --version ]                print version number

  -c [ --config ] arg             Config file to use

  -d [ --data_path ] arg          Path to use for loading any data files the 

                                  application requires.

 

./guppy_aligner 

$ ./guppy_aligner 

 

Usage:

 

  guppy_aligner -i <input fastq path> -s <output SAM path>

    --align_ref <reference file>

 

Command line parameters:

  -z [ --quiet ]              Quiet mode. Nothing will be output to stdout if 

                              this option is set.

  -t [ --worker_threads ] arg Number of worker threads.

  -i [ --input_path ] arg     Path to input fastq files.

  -s [ --save_path ] arg      Path to save fastq files.

  -r [ --recursive ]          Search for input file recursively.

  --trace_categories_logs arg Enable trace logs - list of strings with the 

                              desired names.

  --verbose_logs              Enable verbose logs.

  -a [ --align_ref ] arg      Path to alignment reference.

  --min_coverage arg          Minimum coverage to accept an alignment.

  -h [ --help ]               produce help message

  -v [ --version ]            print version number

  -c [ --config ] arg         Config file to use

  -d [ --data_path ] arg      Path to use for loading any data files the 

                              application requires.

 対応フローセルとキット

> guppy_basecaller  --print_workflows

$ guppy_basecaller  --print_workflows 

Available flowcell + kit combinations are:

flowcell   kit        barcoding config_name

FLO-MIN106 SQK-DCS108           dna_r9.4.1_450bps

FLO-MIN106 SQK-DCS109           dna_r9.4.1_450bps

FLO-MIN106 SQK-LRK001           dna_r9.4.1_450bps

FLO-MIN106 SQK-LSK108           dna_r9.4.1_450bps

FLO-MIN106 SQK-LSK109           dna_r9.4.1_450bps

FLO-MIN106 SQK-LWP001           dna_r9.4.1_450bps

FLO-MIN106 SQK-PCS108           dna_r9.4.1_450bps

FLO-MIN106 SQK-PCS109           dna_r9.4.1_450bps

FLO-MIN106 SQK-PSK004           dna_r9.4.1_450bps

FLO-MIN106 SQK-RAD002           dna_r9.4.1_450bps

FLO-MIN106 SQK-RAD003           dna_r9.4.1_450bps

FLO-MIN106 SQK-RAD004           dna_r9.4.1_450bps

FLO-MIN106 SQK-RAS201           dna_r9.4.1_450bps

FLO-MIN106 SQK-RLI001           dna_r9.4.1_450bps

FLO-MIN106 VSK-VBK001           dna_r9.4.1_450bps

FLO-MIN106 VSK-VSK001           dna_r9.4.1_450bps

FLO-MIN106 SQK-RBK001 included  dna_r9.4.1_450bps

FLO-MIN106 SQK-RBK004 included  dna_r9.4.1_450bps

FLO-MIN106 SQK-RLB001 included  dna_r9.4.1_450bps

FLO-MIN106 SQK-LWB001 included  dna_r9.4.1_450bps

FLO-MIN106 SQK-PBK004 included  dna_r9.4.1_450bps

FLO-MIN106 SQK-RAB201 included  dna_r9.4.1_450bps

FLO-MIN106 SQK-RAB204 included  dna_r9.4.1_450bps

FLO-MIN106 SQK-RPB004 included  dna_r9.4.1_450bps

FLO-MIN106 VSK-VMK001 included  dna_r9.4.1_450bps

FLO-PRO001 SQK-LSK109           dna_r9.4.1_450bps_prom

FLO-PRO001 SQK-DCS109           dna_r9.4.1_450bps_prom

FLO-PRO001 SQK-PCS109           dna_r9.4.1_450bps_prom

FLO-PRO002 SQK-LSK109           dna_r9.4.1_450bps_prom

FLO-PRO002 SQK-DCS109           dna_r9.4.1_450bps_prom

FLO-PRO002 SQK-PCS109           dna_r9.4.1_450bps_prom

FLO-MIN107 SQK-DCS108           dna_r9.5_450bps

FLO-MIN107 SQK-DCS109           dna_r9.5_450bps

FLO-MIN107 SQK-LRK001           dna_r9.5_450bps

FLO-MIN107 SQK-LSK108           dna_r9.5_450bps

FLO-MIN107 SQK-LSK109           dna_r9.5_450bps

FLO-MIN107 SQK-LSK308           dna_r9.5_450bps

FLO-MIN107 SQK-LSK309           dna_r9.5_450bps

FLO-MIN107 SQK-LSK319           dna_r9.5_450bps

FLO-MIN107 SQK-LWP001           dna_r9.5_450bps

FLO-MIN107 SQK-PCS108           dna_r9.5_450bps

FLO-MIN107 SQK-PCS109           dna_r9.5_450bps

FLO-MIN107 SQK-PSK004           dna_r9.5_450bps

FLO-MIN107 SQK-RAD002           dna_r9.5_450bps

FLO-MIN107 SQK-RAD003           dna_r9.5_450bps

FLO-MIN107 SQK-RAD004           dna_r9.5_450bps

FLO-MIN107 SQK-RAS201           dna_r9.5_450bps

FLO-MIN107 SQK-RLI001           dna_r9.5_450bps

FLO-MIN107 VSK-VBK001           dna_r9.5_450bps

FLO-MIN107 VSK-VSK001           dna_r9.5_450bps

FLO-MIN107 SQK-LWB001 included  dna_r9.5_450bps

FLO-MIN107 SQK-PBK004 included  dna_r9.5_450bps

FLO-MIN107 SQK-RAB201 included  dna_r9.5_450bps

FLO-MIN107 SQK-RAB204 included  dna_r9.5_450bps

FLO-MIN107 SQK-RBK001 included  dna_r9.5_450bps

FLO-MIN107 SQK-RBK004 included  dna_r9.5_450bps

FLO-MIN107 SQK-RLB001 included  dna_r9.5_450bps

FLO-MIN107 SQK-RPB004 included  dna_r9.5_450bps

FLO-MIN107 VSK-VMK001 included  dna_r9.5_450bps

FLO-MIN106 SQK-RNA001           rna_r9.4.1_70bps

FLO-MIN106 SQK-RNA002           rna_r9.4.1_70bps

FLO-MIN107 SQK-RNA001           rna_r9.4.1_70bps

FLO-MIN107 SQK-RNA002           rna_r9.4.1_70bps

FLO-PRO001 SQK-RNA002           rna_r9.4.1_70bps_prom

FLO-PRO002 SQK-RNA002           rna_r9.4.1_70bps_prom

 

 

 

実行方法

 フローセル、kit名、入出力(*1)等を指定して実行する。-r (--recursive)をつけるとサブディレクトリも含めてbasecallingされる(*1)。 

guppy_basecaller --flowcell FLO-MIN106 --kit SQK-LSK109 \
--cpu_threads_per_caller 4 --num_callers 4 \
-i fast5/input_dir -s output_dir -r

出力(サブディレクトリ1つ分)

f:id:kazumaxneo:20190310135002j:plain

 

1D^2のbase callingの場合、--fast5_outフラグを立てて上のコマンドを実行し、得られたfast5ファイルをguppy_basecaller_1d2で再びbase callingする2stepで行う(未テスト)。

引用

nanoporetech Guppy 2.3.5 

https://community.nanoporetech.com/protocols/Guppy-protocol-preRev/v/gpb_2003_v1_revh_14dec2018

 

 参考


*1

ツイッターであかまるさんに教えていただきました。