Mercurial > repos > iuc > stacks2_ustacks
view test-data/kmerfilter/kmerfilter.log @ 0:7e5a174bc201 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
author | iuc |
---|---|
date | Mon, 01 Jul 2019 10:57:49 -0400 |
parents | |
children |
line wrap: on
line source
Using a kmer size of 16 Filtering out reads by identifying rare kmers: On. A kmer is considered rare when its coverage is at 15% or below the median kmer coverage for the read. A read is dropped when it contains 13 or more rare kmers in a row. Filtering out reads by identifying abundant kmers: On. Kmer is considered abundant when it occurs 20000 or more times. A read is dropped when it contains 80% or more abundant kmers. Normalizing read depth: Off. Found 1 input file(s). Found 0 paired input file(s). Generating kmer distribution... Generating kmers from file 1 of 1 [R1_0001.fastq] 540 unique k-mers recorded. Filtering reads by kmer frequency... Processing file 1 of 1 [R1_0001.fastq] 5 total reads; -0 rare k-mer reads; -0 abundant k-mer reads; 5 retained reads. Outputing details to log: 'stacks_outputs/kmer_filter.log' 5 total sequences; 0 rare k-mer reads; 0 abundant k-mer reads; 5 retained reads.