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
