Description

Creates a histogram of the number of distinct k-mers having a given frequency.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]

reads (file)

List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]

versions (file)

File containing software versions

versions.yml

hist (file)

KAT histogram of k-mer counts

*.hist

json (file)

KAT histogram summary of distance analysis

*.hist.dist_analysis.json

png (file)

KAT plot of k-mer histogram in PNG format

*.png

ps (file)

KAT plot of k-mer histogram in PS format

*.ps

pdf (file)

KAT plot of k-mer histogram in PDF format

*.pdf

jellyfish_hash (file)

Jellyfish hash file

*-hist.jf*
author
Github user mahesh-panchal
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Tools

kat
GPL v3

KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts

earlham.ac.uk/kat-tools kat.readthedocs.io/en/latest https://github.com/TGAC/KAT10.1093/bioinformatics/btw663