GNU Parallel makes it easy to take advantage of multiple processors at once. I really enjoy using it to parallelize Bash scripts. For example, here’s a pipeline that will generate a reference-based transcriptome from Illumina-sequenced ESTs: . . . Continue reading
Author Archives: Chris
url (Chris)
http://helianth.us now redirects to RLR.
bam file to fastq conversion (Chris)
The GSC supplies our raw sequence reads as bam files. Some programs will take unaligned bam files as input (the bwa is one), but many still do not. A much more flexible format is FASTQ. Here is a link to bam2fastq, a simple little conversion program:
Continue reading