Mercurial > repos > iuc > stacks2_kmerfilter
comparison test-data/kmerfilter/kmerfilter.log @ 0:b2e3553e1be2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
author | iuc |
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date | Mon, 01 Jul 2019 10:58:28 -0400 |
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-1:000000000000 | 0:b2e3553e1be2 |
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1 Using a kmer size of 16 | |
2 Filtering out reads by identifying rare kmers: On. | |
3 A kmer is considered rare when its coverage is at 15% or below the median kmer coverage for the read. | |
4 A read is dropped when it contains 13 or more rare kmers in a row. | |
5 Filtering out reads by identifying abundant kmers: On. | |
6 Kmer is considered abundant when it occurs 20000 or more times. | |
7 A read is dropped when it contains 80% or more abundant kmers. | |
8 Normalizing read depth: Off. | |
9 Found 1 input file(s). | |
10 Found 0 paired input file(s). | |
11 Generating kmer distribution... | |
12 Generating kmers from file 1 of 1 [R1_0001.fastq] | |
13 540 unique k-mers recorded. | |
14 Filtering reads by kmer frequency... | |
15 Processing file 1 of 1 [R1_0001.fastq] | |
16 5 total reads; -0 rare k-mer reads; -0 abundant k-mer reads; 5 retained reads. | |
17 Outputing details to log: 'stacks_outputs/kmer_filter.log' | |
18 | |
19 5 total sequences; | |
20 0 rare k-mer reads; | |
21 0 abundant k-mer reads; | |
22 5 retained reads. |