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。

pATLASflow

 

pATLASflowはplasmid ATLASのマッピング、 mash screen、およびアセンブリメソッドを実行するパイプライン。

 

plasmid ATLAS


インストール

GIthub

#ここでは仮想環境に入れる。
conda create -n pATLASflow nextflow
conda activate pATLASflow
conda instlall -c bioconda -y mash

> nextflow run tiagofilipe12/pATLASflow --help

$ nextflow run tiagofilipe12/pATLASflow --help

N E X T F L O W  ~  version 19.10.0

Launching `tiagofilipe12/pATLASflow` [zen_golick] - revision: 7cec7485d8 [master]

 

===========================================================

                   p A T L A S f l o w

===========================================================

 

Version: 1.1.0

 

Usage:

   nextflow run tiagofilipe12/pATLAS_mash_screen.nf

 

   Nextflow magic options:

       -profile    Forces nextflow to run with docker or singularity.   Default: standard     Choices: standard, singularity,slurm

   Main options:

       --help  Opens this help. It will open only when --help is provided. So, yes, this line is pretty useless since you already know that if you reached here.

       --version   Prints the version of the pipeline script.

       --mash_screen   Enables mash screen run.

       --assembly  Enables mash dist run to use fasta file against plasmid db

       --mapping   Enables mapping pipeline.

   Mash options:

       --kMer  the length of the kmer to be used by mash.   Default: 21

       --pValue    The p-value cutoff. Default: 0.05

   Mash screen exclusive options:

       --identity  The minimum identity value between two sequences. Default: 0.9

       --noWinner  This option allows to disable the -w option of mash screen  Default: false

   Mash dist exclusive options:

       --mash_distance     Provide the maximum distance between two plasmids to be reported.   Default: 0.1

       --shared_hashes     Provide a percentage for the hashesshared between the reference and the query sequence(s).   Default: 0.8

   Reads options:

       --reads The path to the read files. Here users may provide many samples in the same directory. However be assured that glob pattern is unique (e.g. 'path/to/*_{1,2}.fastq').

       --singleEnd Provide this option if you have single-end reads. By default the pipeline will assume that you provide paired-end reads.    Default: false

   Fasta options:

       --fasta     Provide fasta file pattern to be searched by nextflow.  Default: 'fasta/*.fas'

   Bowtie2 options:

       --trim5     Provide parameter -5 to bowtie2 allowing to trim 5' end.    Default: 0

       --cov_cutoff    Provide a cutoff value to filter results for coverage results.  Default: 0.60

 

実行方法

plasmid配列の分類。

nextflow run tiagofilipe12/pATLASflow --assembly --fasta input.fasta

/results/mashdist/にある出力のJSONファイルをpATLASに読み込ませる。

 

引用

GitHub - tiagofilipe12/pATLASflow: A pipeline to run mapping, mash screen and assembly methods for pATLAS.

 

Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data
Tiago F Jesus, Bruno Ribeiro-Gonçalves, Diogo N Silva, Valeria Bortolaia, Mário Ramirez, João A Carriço
Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D188–D194