qbin - bin FASTQ quality scores to reduce file size
qbin --scheme <bin_scheme> < in.fq > out.fq
This program takes a FASTQ file, transforms the quality scores for each sequence into their binned equivalents, and writes the transformed FASTQ entries.
Path to FASTQ input file. If not given, input will be read from STDIN.
Path to FASTQ output file. If not given, output will be written to STDOUT.
The binning scheme to use. Currently three presets are supported:
illumina -- Puts quality scores into one of eight bins:
>= 40 : 40
35-39 : 37
30-34 : 33
25-29 : 27
20-24 : 22
10-19 : 15
2-9 : 6
0-1 : 0
gatk -- Puts quality scores into one of four bins (these were deduced from various Broad Institute documents but are not guaranteed to be the same as those used by GATK):
>= 33 : 40
23-32 : 30
13-22 : 20
3-12 : 10
0-2 : 0
colord -- Puts quality scores into one of four bins according to the CoLoRd preprint (used for long read compression) -- note that CoLoRd uses dynamic output values to keep the same same average quality, but here they are hard-coded):
>= 26 : 40
14-25 : 20
7-13 : 10
1-6 : 3
0 : 0
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Currently unknown. Please submit bug reports to the author.
Jeremy Volkening (jeremy.volkening@base2bio.com)
Copyright 2020-2023 Jeremy Volkening
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.