Description

A tool for filtering reads by given kmers set. Initially created to filter reads with primers and adapters from large datasets.

Requirements

• make
• gcc 4.7 and higher

Usage

./rm_reads <-i raw_data.fastq | -1 raw_data1.fastq -2 raw_data2.fastq> --adapters adapters.dat [-o output_dir --polyG 13 --length 50 --dust_cutoff cutoff --dust_k k -errors 0 -filterN]

-i              input file
-1              first input file for paired reads
-2              second input file for paired reads
-o              output directory (current directory by default)
--polyG, -p     length of polyG/polyC tails (13 by default)
--length, -l    minimum length cutoff (50 by default)
--adapters, -a  file with adapter kmers
--dust_k, -k    window size for dust filter (not used by default)
--dust_cutoff, -c   cutoff by dust score (not used by default)
--errors, -e    maximum error count in match, possible values - 0, 1, 2 (0 by default)
--filterN, -N   allow filter by N's in reads

Input files

Tools takes files with reads in fastq format as input. You can also use paired end reads. In case if you are using paired end reads, please, make sure that all reads from first file have correct pairs in second file.

Output files

Tool creates following files in output directory: input_prefix.ok.fastq file with correct reads input_prefix.fitered.fastq file with reads, containing adapter kmers, N's, polyG/polyC tails or filtered by dust filter. Reason why read was filtered is given in the read id. input_prefix.se.fastq for paired reads only. File with correct reads which have incorrect pair.

Project page

Last version of project can be found at https://github.com/allivi/rm_reads