Comparing aligners

When analyzing genomic data, we first need to align to the genome. There are a lot of possible choices in this, including BWA (medium choice), stampy (very accurate) and bowtie2 (very fast). Recently a new aligner came out, NextGenMap. It claims to be both faster and deal with divergent read data better than other methods. Continue reading

Our favourite text editors (Rose)

I hope we can start a conversation about this because a good text editor can make a big difference to a newbie, so PLEASE REPLY!!! I wanted to proselytise about Npp, but it only runs on Windows. So if you use a different OS, please make that BLEEDINGLY OBVIOUS.

Notepad++ (WINDOWS )

I’ve tried a numerous text editors over the years (like Context), but Notepad++ (Npp) is easily my favourite. It only runs on Windows, but I use it to export Unix formatted files routinely. You can set shortcut keys to change formats very easily. Npp can highlight lots of languages, including R, perl and unix. You can also define your own languages for highlighting – I did that to make my Migrate parameter files easier to read.
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