Various Developments in the Bioinformatics World

The world of bioinformatics did not stand still, while we were away. Thanks to twitter, catching up is lot easier than the past.

Here is a summary of important releases -

(i) Very cool - Using Next-gen Sequencing to Unravel Outbreaks of Infectious Disease

(ii) Genome-guided Trinity - a cufflink alternative? (ht: @genetic_blog)

(iii) Minia is now open source. Thanks Rayan.

(iv) Cortex variation assembler (ht: CTB) -

We have developed a software package, Cortex, designed for the analysis of genetic variation by de novo assembly of multiple samples. This allows direct comparison of samples without using a reference genome as intermediate, and incorporates discovery and genotyping of SNPs, indels and larger events in a single framework.

(v) A good discussion on nanopore sequencing at reddit (ht: Jason Chin)

(vi) We are not sure, whether we posted about this before. BGI developed method for incorporating very long PE reads.

(vii) How much sequencing is needed for de novo assembly? (blog post from C. Titus Brown).

(viii) Is $1000 genome a bait-and-switch?

(ix) Illumina 150PE Rocks, while

Helicos files for bankruptcy. Also see here.

(ix) Two interesting articles on changing how scientists communicate -

Scientific Utopia: I. Opening scientific communication

Scientific Utopia: II. Restructuring incentives and practices to promote truth over publishability