Trimming tool

Question

[GeneC]

Hello,

Is there any free standing tool kit to trim extra bases or adapter sequences from fastq files?

Thanks

[Ram]

Please do a few simple Google searches before asking others for help.

Answer 1

[GenoMax]

There are plenty. bbduk.sh from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ ) , fastp (LINK), cutadapt (LINK) and trimmomatic (LINK).

Answer 2

[ntsopoul]

I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore

Here is the script I am using for paired-end sequencing

for i in $(ls *R1* | sed s/_R1.fastq.gz// | sort -u); 

do

trim_galore --paired ${i}_R1.fastq.gz ${i}_R2.fastq.gz -q 20 -o ./galore-trimmed --fastqc --cores 6 --stringency 3

done