Germinant Receptors in P. larvae - Bioinformatics

From 4-13-15.

Downloaded Stampy & BWA from http://www.well.ox.ac.uk/software-download-registration.

From the website:

Description: Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome. It's recommended for most workflows, including those for genomic resequencing, RNA-Seq and Chip-seq. Stampy excels in the mapping of reads containing that contain sequence variation relative to the reference, in particular for those containing insertions or deletions. It can map reads from a highly divergent species to a reference genome for instance. Stampy achieves high sensitivity and speed by using a fast hashing algorithm and a detailed statistical model. Stampy has the following features: Maps single, paired-end and mate pair Illumina reads to a reference genome Fast: about 20 Gbase per hour in hybrid mode (using BWA) Low memory footprint: 2.7 Gb shared memory for a 3Gbase genome High sensitivity for indels and divergent reads, up to 10-15% Low mapping bias for reads with SNPs Well calibrated mapping quality scores Input: Fastq and Fasta; gzipped or plain Output: SAM, Maq's map file Optionally calculates per-base alignment posteriors Optionally processes part of the input Handles reads of up to 4500 bases The reference paper for the package can be found here. I plan to use Stampy & BWA to map all my downloaded sequences to a reference strain of P. larvae DSM 25430, which I have also downloaded the fasta file from NCBI for. //EWW