Quickly compute statistics over a fasta file in windows.
Input
name:type
description
pattern
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
fasta{:bash}
:file
FASTA file
*.{fa,fasta,fna}
Output
name:type
description
pattern
freq{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
fw_out/*_freq_windows.tsv{:bash}
:file
TSV file with frequencies and statistics
*.{tsv}
mononuc{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
fw_out/*_mononuc_windows.tsv{:bash}
:file
TSV file with mononucleotide counts
*.{tsv}
dinuc{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
fw_out/*_dinuc_windows.tsv{:bash}
:file
TSV file with dinucleotide counts
*.{tsv}
trinuc{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
fw_out/*_trinuc_windows.tsv{:bash}
:file
TSV file with trinucleotide counts
*.{tsv}
tetranuc{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
fw_out/*_tetranuc_windows.tsv{:bash}
:file
TSV file with tetranucleotide counts
*.{tsv}
versions{:bash}
versions.yml{:bash}
: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
