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 article...

Flashcard Fridays – The 1000 Genomes Project

05/07/2013

After the “whole” genome sequence of Craig Venter and James Watson were published and newly developed sequencing technologies made the runtime and price of whole genome and whole exome sequencing acceptable, 1000 Genomes was the first public sequencing project that sequenced a high amount of individuals. The aim of the...

Workflow Wednesdays – Reference sequence – Part 1. Indexing

03/07/2013

I’ve already written some posts about fasta files and reference sequences (about file formats and where to get reference sequences. You might remember from my first “Workflow Wednesdays” post, that I selected short reads created with the three major sequencing technologies from the same E. coli strain: strain K-12 substrain...

Bioinformatics for Beginners – File Formats Part 2. – Short reads

01/07/2013

Short reads can be stored in several different formats. The best known (and most used) of these is the fastq format, which contains both the base and quality values for each read within a single file. Note, that there are different fastq formats around. The main difference between these is...

Flashcard Fridays – SEQanswers

28/06/2013

If you are looking for an open access, interactive knowledge base and forum about basically anything NGS related, check out SEQanswers! With more than 35000 registered members (and most likely even more “lurkers”), it”s possibly the largest and fastest growing NGS community around.