Filtering mitochondrion reads from FastQ files

Question

[javanokendo]

I have fastq files which contains mitochondrion reads. I want to filter out the mitochondrion reads then do the assembly on the resultant reads. Is there a way this can be achieved? Any pointer will be appreciated.

[samuel.a.odonnell]

Is there a particular reason you need to remove them prior to assembly? Will they cause an issue during assembly?

Answer 1

[GenoMax]

You could simply align your data (use any aligner you like) to the mitochondrial genome and collect reads that do not map. Some aligners can directly separate them for others you may need to filter them out of the resulting BAM alignment file.

[javanokendo]

The following line of code enabled me to filter out mitochondrion reads and I got what I was expecting. I am living it hare because it will help someone.

bbsplit.sh in=HGLGLDSX3_19242446_S3_L001_R1_001.fastq.gz in2=HGLGLDSX3_19242446_S3_L001_R2_001.fastq.gz ref=paradisefishMtsequence.fasta basename=out_%.fastq.gz outu1=mat1.fastq.gz outu2=mat2.fastq.gz