Trimbadseq

This is a perl script that trims out undesired “bad sequences” from paired fastq files such as poly-N or poly-A sequences.

• You can apply this before applying tools like trimmomatic.
• You define what pattern(s) of sequences are “bad”.
  • Use simple perl regular expressions.
• For each read, the longest contiguous “good sequence” is returned if it is not “too short”.
  • You define the length of the shortest accepted read.
• Reads with no accepted contiguous “good sequences” are filtered out completely.
• If only one read in a pair has an accepted “good sequence”, that one is included in the “unpaired reads” output file.

Figure 1 shows an example where the length of the shortest accepted sequence is 25 bases.

Download

Files are available this github page.

Download the perl script: trimbadseq2.pl

Sample data

Download sample fastq files (i_1.fq and i_2.fq) this github page.

Try running this on these sample fastq files and check the output files:

perl trimbadseq2.pl i_1.fq i_2.fq o_1.fq o_2.fq o_u.fq 20 “A{10,}” “N{3,}”

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