Crate fasten_shuffle
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Interleaves reads from either stdin or file parameters.
Many fasten executables are aware of paired end reads but they need to be in interleaved format. This script transforms R1 and R2 reads into interleaved format.
Examples
Shuffling
Simple transformation of R1 and R2 into interleaved
cat file_1.fastq file_2.fastq | fasten_shuffle > interleaved.fastq
fasten_shuffle -1 file_1.fastq -2 file_2.fastq > interleaved.fastq
interleave R1 and R2 and pipe it into another executable with –paired-end
cat file_1.fastq file_2.fastq | fasten_randomize --paired-end | head -n 8 > random-pair.fastq
… or to another executable with –paired-end
cat file_1.fastq file_2.fastq | fasten_sample --paired-end --frequency 0.2 > downsample.20percent.fastq
Deshuffling
cat interleaved.fastq | fasten_shuffle -d -1 1.fastq -2 2.fastq
Usage
Usage: fasten_shuffle [-h] [-n INT] [-p] [-v] [-d] [-1 1.fastq] [-2 2.fastq]
Options:
-h, --help Print this help menu.
-n, --numcpus INT Number of CPUs (default: 1)
-p, --paired-end The input reads are interleaved paired-end
-v, --verbose Print more status messages
-d, --deshuffle Deshuffle reads from stdin
-1 1.fastq Forward reads. If deshuffling, reads are written to
this file.
-2 2.fastq Forward reads. If deshuffling, reads are written to
this file.