A collection of command line tools to modify fastq files (http://en.wikipedia.org/wiki/FASTQ_format).
Scripts are designed to be saved as runnable jars and run from terminal using java -jar SCRIPT ARGUMENTS. Use -Xms and -Xmx arguments to dedicate more memory to java (java -Xms4000m -Xmx12000m -jar SCRIPT ARGUMENTS). To get script specific information, please call the scripts without any arguments.
Contained scripts:
- FilterForPairs:
Description: Filters two fastq files for entries with matching name.
Rational: Some read alignmeners (GSNAP, Mapsplice) do not tolerate fastq entries contained in only one of the two paired end sequencing fastq files. These single entries are generated for example by adaptor trimming using cutadapt. To allow mapping, this script removes fastq entries present in only one of the paired end fastq files.
Output: Fastq files matching input names appended by "_matched".
Usage: java -jar filterForPairs /path/to/fastq1 /path/to/fastq2