Sanjeet Kumar's repositories
SHIVGAMI
SHIVGAMI is a tool, which run blastX process by assembling the CPU cores from avaialble Linux computing units.
homoplasyFinder
A tool to identify and annotate homoplasies on a phylogeny and sequence alignment
bioinformatics-one-liners
Bioinformatics one liners from Ming Tang
abricate
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
MrBayes
MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:
biocode
Bioinformatics code libraries and scripts
FastANI
Fast Whole-Genome Similarity (ANI) Estimation
pgap
NCBI Prokaryotic Genome Annotation Pipeline
ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
legen_pipeline
Lactobacillus Evolutionary Genomics Pipeline
progenomics
A toolkit for prokaryotic comparative genomics
proclasp
Classification of prokaryotic genomes on the species level
tidytypes
Functions to Download Type Strain Names
spades
SPAdes Genome Assembler
nanostat
Create statistic summary of an Oxford Nanopore read dataset
qiime
Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
Kraken_db_install_scripts
Updated Kraken DB install scripts to cope with new-ish NCBI structure
to-gff
Convert .gbk or .embl to .gff (and optionally .fa) (required for QUAST)