PacBioのCCSコマンド - macでインフォマティクス

マニュアルより

サーキュラー・コンセンサス・シーケンス（CCS）解析は、環状化された単一DNA分子（SMRTbell®テンプレート）を複数回「パス」してコンセンサス配列を計算する。CCS解析では、利用可能なパス数を考慮して最適なコンセンサス結果を得るためにArrowフレームワークを使用する。

https://ccs.how/

FAQ

https://ccs.how/faq/

Manual

https://www.pacb.com/wp-content/uploads/SMRT_Tools_Reference_Guide_v11.0.pdf#page=8.08

HPより転載

インストール

Github

#conda (link)
mamba install bioconda::pbccs -y

> ccs -h

ccs - Generate circular consensus sequences (ccs) from subreads.

Usage:

ccs [options] <IN.subreads.bam|xml> <OUT.ccs.bam|fastq.gz|xml>

IN.subreads.bam|xml FILE Subreads (.subreads.bam or .subreadset.xml).

OUT.ccs.bam|fastq.gz|xml FILE Consensus reads (.bam, .fastq.gz, or .consensusreadset.xml).

Input Filter Options:

--min-passes INT Minimum number of full-length subreads required to generate CCS for a ZMW. [3]

--min-snr FLOAT Minimum SNR of subreads to use for generating CCS [2.5]

--top-passes INT Pick at maximum the top N passes for each ZMW. [60]

Draft Filter Options:

--min-length INT Minimum draft length before polishing. [10]

--max-length INT Maximum draft length before polishing. [50000]

Chunking Options:

--chunk STR Operate on a single chunk. Format i/N, where i in [1,N]. Examples: 3/24 or 9/9

--max-chunks Determine maximum number of chunks.

Model Override Options:

--model-path STR Path to a chemistry model file or directory containing model files.

--model-spec STR Name of chemistry or model to use, overriding default selection.

Processing Options:

--by-strand Generate a consensus for each strand.

--hd-finder Enable heteroduplex finder and splitting

--skip-polish Only output the initial draft template (faster, less accurate).

--all Emit all ZMWs.

--subread-fallback Emit a representative subread, instead of the draft consensus, if polishing failed.

--all-kinetics Calculate mean pulse widths (PW) and interpulse durations (IPD) for every ZMW.

--hifi-kinetics Calculate mean pulse widths (PW) and interpulse durations (IPD) for every HiFi read.

Output Filter Options:

--min-rq FLOAT Minimum predicted accuracy in [0, 1]. [0.99]

Output Files Options:

--report-file FILE Where to write the results report.

--report-json FILE Where to write the results report as json.

--metrics-json FILE Where to write the zmw metrics as json.

--suppress-reports Do not generate report or metric files per default, only those requested.

-h,--help Show this help and exit.

--version Show application version and exit.

-j,--num-threads INT Number of threads to use, 0 means autodetection. [0]

--log-level STR Set log level. Valid choices: (TRACE, DEBUG, INFO, WARN, FATAL). [WARN]

--log-file FILE Log to a file, instead of stderr.

This program comes with ABSOLUTELY NO WARRANTY; it is intended for

Research Use Only and not for use in diagnostic procedures.

PacBioのSMRTbellテンプレートの BAM formatファイル (.subreads.bam)1 つを指定する。最低３回のパスを通ったリードのみを使用。

ccs movie.subreads.bam movie.ccs.bam --min-passes 3

--chunk <STR> Operate on a single chunk. Format i/N, where i in [1,N]. Examples: 3/24 or 9/9
--min-passes <INT> Minimum number of full-length subreads required to generate CCS for a ZMW. [3]

fastq出力

ccs movie.subreads.bam out.fq.gz

allをつけると無駄なポリッシングを避けつつ、高精度リードが生成できない場合でも、代表的なサブリードを出力する。

ccs movie.subreads.bam out.fq.gz

詳しくはマニュアルのP11参照。

引用

https://ccs.how/

参考

https://www.pacb.com/wp-content/uploads/SMRT_Tools_Reference_Guide_v11.0.pdf

のPacBio command-line toolsのページ参照