Workflow Wednesdays – Coverage analysis 2. and other alignment statistics

02/10/2013

As I promised last week, I’ll show you some command line based alignment analysis tools this week. As there are basically an endless number of methods for generating alignment statistics, feel free to share additional tips and tricks in the comment section!

Workflow Wednesdays – Sorting alignments

11/09/2013

Most variant calling softwares require sorted alignments as an input. There are two main ways to sort a SAM or BAM file: you can sort the lines by read names or you can sort the aligned reads by leftmost coordinates.

Workflow Wednesdays – Alignments – Format conversion

04/09/2013

I could go on forever and ever about different short read aligners, but I think you get the gist of it. So let’s talk about alignment files! Most modern reference based aligners produce their output in sam format. If you’re not familiar with this file format, check out my...

Workflow Wednesdays – Creating alignments – BWA

14/08/2013

Drumroll! Hurrah! We are finally going to do some alignments today! BWA is probably the most widely used short read aligner ever. By now, it’s even part of the official Illumina analysis pipeline. BWA actually contains three different aligner algorithms. We’ll try all of these today.

Bioinformatics for Beginners – File Formats Part 3. – Alignments

08/07/2013

The generally used file formats for sequence based alignments are the SAM and BAM formats. These files can contain information about mapped and unmapped reads, the contigs of the reference sequence that was used and many more things. SAM You can find the SAM format specification here and the...