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
#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]
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p A T L A S f l o w
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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
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