rob-p / fcseqtk

Fork of SeqTK adapted for FusionCatcher

Introduction

Seqtkfc is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip. Seqtkfc is fork of seqtk which was adapted for use with FusionCatcher.

Seqtkfc Examples

• Convert FASTQ to FASTA:

    fcseqtk seq -a in.fq.gz > out.fa
  

• Convert ILLUMINA 1.3+ FASTQ to FASTA and mask bases with quality lower than 20 to lowercases (the 1st command line) or to N (the 2nd):

    fcseqtk seq -aQ64 -q20 in.fq > out.fa
    fcseqtk seq -aQ64 -q20 -n N in.fq > out.fa
  

• Fold long FASTA/Q lines and remove FASTA/Q comments:

    fcseqtk seq -Cl60 in.fa > out.fa
  

• Convert multi-line FASTQ to 4-line FASTQ:

    fcseqtk seq -l0 in.fq > out.fq
  

• Reverse complement FASTA/Q:

    fcseqtk seq -r in.fq > out.fq
  

• Extract sequences with names in file name.lst, one sequence name per line:

    fcseqtk subseq in.fq name.lst > out.fq
  

• Extract sequences in regions contained in file reg.bed:

    fcseqtk subseq in.fa reg.bed > out.fa
  

• Mask regions in reg.bed to lowercases:

    fcseqtk seq -M reg.bed in.fa > out.fa
  

• Subsample 10000 read pairs from two large paired FASTQ files (remember to use the same random seed to keep pairing):

    fcseqtk sample -s100 read1.fq 10000 > sub1.fq
    fcseqtk sample -s100 read2.fq 10000 > sub2.fq
  

• Trim low-quality bases from both ends using the Phred algorithm:

    fcseqtk trimfq in.fq > out.fq
  

• Trim 5bp from the left end of each read and 10bp from the right end:

    fcseqtk trimfq -b 5 -e 10 in.fa > out.fa
  

• Keep first 50bp from the left end of each read by trimming the right end:

    fcseqtk trimfq -B 50 in.fq > out.fq
  

• Keep last 50bp from the right end of each read by trimming the left end:

    fcseqtk trimfq -E 50 in.fq > out.fq
  

• Trim 5bp from left end and keep next 50bp from left end of each read:

    fcseqtk trimfq -B 50 -b 5 in.fq > out.fq
  

• Trim 5bp from right end and keep the 50bp from right end of each read:

    fcseqtk trimfq -E 50 -e 5 in.fq > out.fq
  

• Trim 5bp from right end and keep the 50bp from right end of each read and if trimmed read length ends up having less the 20bp then the first 20 bp should be kept only:

    fcseqtk trimfq -E 50 -e 5 -l 20 in.fq > out.fq