bowtie2: Relaxed Parameters for Generous Alignments to Metagenomes
Even `bowtie2`’s `–very-sensitive-local` option can be a little grumpy. Here’s how I make `bowtie2` a little more relaxed for alignment of more dissimilar sequences, particularly for my work on metagenomes.
Bioinformatics is a disorganised disaster and I am too. So I made a shell.
I am not a very organised bioinformatician, and despite your best efforts, you probably aren’t either. I’ve written a tool called `chitin` that tries to keep me, and bioinformatics more organised.
Goldilocks: A tool for identifying genomic regions that are “just right”
I’m published! I’m a real scientist now! Check out the application note on Bioinformatics.
How (not) to subset a BAM for GATK
I wanted a BAM that contained reads aligned to just one of the many contigs the file contained. As usual, I made this much more difficult than it really ought to have been.
Duplicate definition error with GATK PrintReads and MalformedReadFilter
This afternoon I wanted to quickly check whether some reads in a BAM would be filtered out by the GATK `MalformedReadFilter`. Turns out that GATK is pretty unforgiving if you forget that filter is automatically applied by `PrintReads`.
Grokking GATK: Common Pitfalls with the Genome Analysis Tool Kit (and Picard)
Recently I’ve been following the GATK DNASeq Best Practice Pipeline for my limpet sequence data. Here are some of the mistakes I made and how I made them go away.
As a curious and nosy individual who likes to know everything, I wrote a script dubbed memblame which is responsible for naming and shaming authors of “inefficient”1 jobs at our cluster here in IBERS. It takes time, often days, sometimes longer, of patience to see large-input jobs executed on a node on the compute cluster […]