This tool divides a fastq file into smaller fastq files, based on the number of output files specified.
This tool divides a fastq file into smaller fastq files, based on the number of output files specified. For ecample, if one specifies 5 output files, it will split the fastq into 5 files of equal size. This can be very useful if one wants to use the chunking option in a pipeline: FastqSplitter can generate the exact number of fastq files (chunks) as needed.
FastqSplitter will read groups of reads (100 reads per group) and distribute this evenly over the output FASTQ files. FastqSplitter will iterate over all the output files while writing the read groups.
Example: A fastq file is split with a group size of 100 and three output files. read 1-100 will be assigned to output1 read 101-200 will be assigned to output2 read 201-300 will be assigned to output3 read 301-400 will be assigned to output1 read 401-500 will be assigned to output2 etc.
This will make sure the output fastq files are of equal size and there is no positional bias in each output file.
For documentation and manuals visit our github.io page: https://biopet.github.io/fastq-splitter
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install biopet-fastqsplitter
and update with:
conda update biopet-fastqsplitter
or use the docker container:
docker pull quay.io/biocontainers/biopet-fastqsplitter:<tag>
(see biopet-fastqsplitter/tags for valid values for
biopet-fastqsplitter is a Java program that comes with a custom wrapper shell script. By default ‘no default java option’ is set in the wrapper. The command that runs the program is ‘biopet-fastqsplitter’. If you want to overwrite it you can specify memory options directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence. For example run it with ‘biopet-fastqsplitter -Xms512m -Xmx1g’.