What it does
PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets. This tool allow to process the sequences with filtering and trimming. More information on PRINSEQ manual.
The input file is sequence file in fastq format (sequences and quality):
@HWI-M00234:263:000000000-ADM55:1:1101:7508:4067 1:N:0:ATCACG GGTGCACTAGGATCGTAGTTGGCTACTTTCCCGTTTTCAATGTATACGCAAGGTACACGGTCAGCGGT + CCCCCGFGED8DDCAFDAEE9DFGGGG9CFAFFCC@@CFGFGGCGFGG>GGGFFGDGEFFEFG8>4GF
The parameters are numerous in PRINSEQ given the wanted treatments.
Several filter treatments are proposed:
- Filters based on sequence length
- Filters based on quality score
- Filters based on base content
And several trimming treatments eliminate sequence parts:
- Trim of ends
- Trim of tails
- Trim based quality score
All these treaments can be customed using proposed parameters.
The output file is a sequence file with sequences and quality from input file which have undergone filter and trimming.