catfishq

Takes paths to an arbritary number of zipped and unzipped FASTQ files and/or folders containing zipped or unzipped FASTQ files, concatenates them and prints them to standard out (default) or an unzipped output file.

Supported file extensions are: '*.fastq', '*.fastq.gz', '*.fasta', '*.fasta.gz', '*.fa', '*.fa.gz', '*.fq', '*.fq.gz'

May also be used to filter FQ reads by read ID, read length, q-score, and min/max sequencing time.

Install

pip install catfishq

Examples

Check full command list:

$ catfishq --help;

Merge all FQ files within a target directory:

$ catfishq test/ > test.fastq;

Merge all FQ files within a target directory and its sub-directories (recurive):

$ catfishq -r test/ > test.fastq;

Merge the first 1000 reads:

$ catfishq -n 1000 test/ > test_1st_1000.fastq;

Merge reads with a length >=50bp and a q-score >=10:

$ catfishq -l 50 -q 10 -l test/ > test_filt.fastq;

Merge reads collected <60mins from sequencing start:

catfishq --min-sequencing-time 0 --max-sequencing-time 60 test/ > test_60_min.fastq;  #merge reads

Note that when looping catfishq over multiple folders from the same run, it is quicker to grab the start time via --print-start-time and providing it to catfishq via --start-time "$timestamp".

$ t0="$(catfishq --print-start-time test1)";
catfishq --max-sequencing-time 60 --start-time "$t0" test1/ > test1_60_min.fastq;
catfishq --max-sequencing-time 60 --start-time "$t0" test2/ > test2_60_min.fastq;