Trimming tool
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27 days ago
GeneC • 0

Hello,

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

Thanks

Trimming • 394 views
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Please do a few simple Google searches before asking others for help.

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27 days ago
GenoMax 143k

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).

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27 days ago
ntsopoul ▴ 60

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
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