Description

Multiple sequence alignment using MAFFT

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

fasta (file)

FASTA file containing the sequences to align. May be gzipped or uncompressed.

*.{fa,fasta}{.gz,}

meta2 (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

add (file)

FASTA file containing sequences to align to the sequences in fasta using --add. May be gzipped or uncompressed.

*.{fa,fasta}{.gz,}

meta3 (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

addfragments (file)

FASTA file containing sequences to align to the sequences in fasta using --addfragments. May be gzipped or uncompressed.

*.{fa,fasta}{.gz,}

meta4 (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

addfull (file)

FASTA file containing sequences to align to the sequences in fasta using --addfull. May be gzipped or uncompressed.

*.{fa,fasta}{.gz,}

meta5 (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

addprofile (file)

FASTA file containing sequences to align to the sequences in fasta using --addprofile. May be gzipped or uncompressed.

*.{fa,fasta}{.gz,}

meta6 (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

addlong (file)

FASTA file containing sequences to align to the sequences in fasta using --addlong. May be gzipped or uncompressed.

*.{fa,fasta}{.gz,}

compress (boolean)

Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded.

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

fas (file)

Aligned sequences in FASTA format. May be gzipped or uncompressed.

*.fas{.gz,}
included in
ampliseq multiplesequencealign pathogensurveillance phyloplace
maintainers
Github user MillironX
Github user Joon-Klaps
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

mafft
BSD

Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform

mafft.cbrc.jp/alignment/software mafft.cbrc.jp/alignment/software/manual/manual https://mafft.cbrc.jp/alignment/software/source.html 10.1093/nar/gkf436

pigz

Parallel implementation of the gzip algorithm.

zlib.net/pigz zlib.net/pigz/pigz.pdf