Category: Tools

bowtie2: Relaxed Parameters for Generous Alignments to Metagenomes

   Sam Nicholls    No Comments yet    Tools

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.

   Sam Nicholls    No Comments yet    Bioinformatics, chitin

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.


Duplicate definition error with GATK PrintReads and MalformedReadFilter

   Sam Nicholls    One Comment    Tools

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`.


`memblame`

   Sam Nicholls    No Comments yet    System Administration, Tools

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 […]