Bioinformatics relevant research topics are:
genomic scale studies
endogenous mechanisms of mutations, germ line and somatic
computational aspects of immunology in cancer
signalling networks
three-dimensional organization of information in...
Breitbart’s lab has created a new branch of biology called metagenomics in which one can sample and sequence genetic material collected from the environment.
Breitbart lab is located in the College of Marine Science at the University of South...
Job Description
We are looking for a motivated application scientist to help evaluate, compare, and develop next generation sequencing (NGS) data analysis methods. The successful candidate should be able to quickly understand the state-of-art...
kallisto
Transcript abundance quantification from RNA-seq data (uses pseudoalignment for rapid determination of read compatibility with targets)
Software (C++)
https://pachterlab.github.io/kallisto/
Sailfish
Estimation of isoform abundances...
github.com - Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS).
Ra is in...
github.com - HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for...
bix.ucsd.edu - BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion...
gite.lirmm.fr - An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are...
