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。

Smith-Watermanのアライナー swalign

 

 インストール

mac os10.14の miniconda2-4.3.14環境でテストした。

本体 Github

#Anaconda環境でcondaを使い導入
conda install -c bioconda swalign

> swalign

$ swalign

 

Simple Smith-Waterman aligner

 

Usage: swalign {options} ref query

 

Reference and query arguments can either be written on the command-line, read

from stdin, or read as FASTA format files. If there is more than one sequence

in the reference FASTA file, the query will be aligned to all reference

sequences and only the best scoring alignment will be displayed. If more than

one sequence is in a query FASTA file, each query sequence will be aligned to

the reference.

 

Alignments will be made in both forward and reverse directions.

 

Options:

  -m N              Match score (default: 2)

  -mm N             Mismatch penalty (default: 1)

  -gap N            Gap penalty (default: 1)

  -gapext N         Gap extension penalty (default: 1)

  -gapdecay N       Decay the gap extension penalty (default: 0.0)

  -wrap N           Wrap alignments when they are longer than N bases

  -global           Perform a global alignment (experimental)

  -query            Align the full query sequence (mix of local/global)

  -summary fname    Write a summary files of match locations (tab-delimited)

  -useregion        Use regions for coordinates if included in FASTA ref

 

Example:

    ~$ swalign AAGGGGAGGACGATGCGGATGTTC AGGGAGGACGATGCGG

 

 

実行方法

swalign ref.fa query.fa > align

 

 

引用

GitHub - mbreese/swalign: Smith-Waterman local aligner