Description

Quickly compute statistics over a fasta file in windows.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

fasta (file)

FASTA file

*.{fa,fasta,fna}

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

freq (file)

TSV file with frequencies and statistics

*.{tsv}

mononuc (file)

TSV file with mononucleotide counts

*.{tsv}

dinuc (file)

TSV file with dinucleotide counts

*.{tsv}

trinuc (file)

TSV file with trinucleotide counts

*.{tsv}

tetranuc (file)

TSV file with tetranucleotide counts

*.{tsv}
author
Github user muffato
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Tools

fastawindows
MIT

fasta_windows is a tool written for Darwin Tree of Life chromosomal level genome assemblies. The executable takes a fasta formatted file and calculates some statistics of interest in windows

github.com/tolkit/fasta_windows