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.

Flashcard Fridays – How accurate is next generation sequencing?

02/08/2013

As for most unspecific questions, my best answer is “it depends”.* And it depends on a lot of things: the sequencing platform, the experiment design, the lab protocol, the quality of the biological sample, the mood of the lab tech, etc. I could go on and on and on...

Workflow Wednesdays – Part 3. Read preprocessing – Read quality control 2. – QC results

26/06/2013

Text output Both FastQC and PRINSEQ can generate some basic statistics for each fastq file. For FASTQC these are the following: “Total Sequences” (i.e. the number of reads), “Filtered Sequences”, “Sequence Length” (read length range) and “%GC” (average GC-content). Additionally, tables for “Overrepresented sequences” and “Kmer content” are generated....

Workflow Wednesdays – Part 3. Read preprocessing – Read quality control 1. – Running QC tools

19/06/2013

Read quality control tools can provide very useful information about the the success of your sequencing experiment, without the need to run time consuming alignments and variant calls. Based on read length, per base quality, base content and other basic statistics you can find out a lot about your...

Workflow Wednesdays – Part 2. Read preprocessing – File format conversion

12/06/2013

A little bit about the Linux/Unix command line First of all, let me tell you about the working environment I will use for this data analyis series. I have a laptop with a 4 core Intel processor and 2*4G RAM. I use 64-bit Ubuntu (version 13.04 to be exact)....