Senthil Murugapiran's repositories
BURST
An ultrafast optimal aligner for mapping large NGS data to large genome databases.
DAS_Tool
DAS Tool
dotfiles
XMonad, acme plumb configuration files (OpenBSD/Slackware)
drep
Rapid comparison and dereplication of genomes
examples
example applications built using bíogo
Gleesso_Pipeline
Inference of co-abundance graph for metagenomic species
krakenuniq
🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
MMseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
mothur
Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Immunology at The University of Michigan. This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
mothur.github.io
wiki for the mothur software package
org-transclusion
Emacs package to enable transclusion with Org Mode
phyloseq
phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
phyloseq-extended
Various customs functions written to enhance the base functions of phyloseq. Most of them are used in the formation "Métagénomique 16S" provided by the platforms Migale and Genotoul
prokka
:zap: :aquarius: Rapid prokaryotic genome annotation
Ragout
Chromosome-level scaffolding using multiple references
Rarefaction
Rarefaction scripts
ReSeq
More realistic simulator for genomic DNA sequences from Illumina machines that achieves a similar k-mer spectrum as the original
RGAAT_v2
Add multiple thread function for genome comparison
SCORE
SCORE - a consensus tool for detecting differentially expressed genes in bacteria
SequenceTools
Programs used in the lab for various tasks
simka
Simka is a comparative metagenomics method dedicated to NGS datasets.
simuscop
a novel next-generation sequencing simulator using position and genomic contexts based error profiles
trinityrnaseq
Trinity RNA-Seq de novo transcriptome assembly
wgsim
Reads simulator
wtdbg2
A fuzzy Bruijn graph approach to long noisy reads assembly