Software for Quality Check of reads

Question

[utkarsh.sood]

Hi,

I have reads generated for metagenome sequence using Illumina Miseq paired-end reads with the read length of 250 bp. I want to perform the quality check for the obtained sequence.

Could anyone please let me know the software that can be used? I read about Prinseq standalone version but it has various options. I am a little confused about which parameters to use.

I want to remove sequences that have Phred score below 20.

Thanks

Answer 1

[GenoMax]

FastQC for general QC.

bbduk.sh from BBMap for scanning and trimming of data. Some quality related options.

trimq=6             Regions with average quality BELOW this will be trimmed,
                    if qtrim is set to something other than f.  Can be a 
                    floating-point number like 7.3.
maxlength=          Reads longer than this after trimming will be discarded.
                    Pairs will be discarded only if both are longer.
minavgquality=0     (maq) Reads with average quality (after trimming) below 
                    this will be discarded.
maqb=0              If positive, calculate maq from this many initial bases.
minbasequality=0    (mbq) Reads with any base below this quality (after 
                    trimming) will be discarded.