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

freq

meta:map

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

]

fw_out/*_freq_windows.tsv:file

TSV file with frequencies and statistics

*.{tsv}

mononuc

meta:map

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

]

fw_out/*_mononuc_windows.tsv:file

TSV file with mononucleotide counts

*.{tsv}

dinuc

meta:map

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

]

fw_out/*_dinuc_windows.tsv:file

TSV file with dinucleotide counts

*.{tsv}

trinuc

meta:map

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

]

fw_out/*_trinuc_windows.tsv:file

TSV file with trinucleotide counts

*.{tsv}

tetranuc

meta:map

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

]

fw_out/*_tetranuc_windows.tsv:file

TSV file with tetranucleotide counts

*.{tsv}

versions

versions.yml:file

File containing software versions

versions.yml

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