HTS (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



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

本体 Github

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.



  -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







swalign ref.fa query.fa > align




GitHub - mbreese/swalign: Smith-Waterman local aligner