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baga

Bacterial and Archaeal Genome Analyser

bash-oneliner

Bash Oneliner learning station. This blog will focus on bash commands for parsing biological data, which are tsv files(tab-separated values); some of the commands are for Ubuntu system maintaining. I apologize that there won't be any citation of the code, but they are probably from dear Google and Stackoverflow. Not all the code here are oneliner (if the ';' counts..). English and bash are not my first language, so... correct me anytime, tks!!

bcftools

This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib

is_mapper

IS mapping software

jvarkit

Java utilities for Bioinformatics

mlst_check

my_silly_scripts

neat

NExt generation Analysis Toolbox

pan-genome-visualization

phd_scripts

Material Suplementario, scripts

programmingassignment2

Repository for Programming Assignment 2 for R Programming on Coursera

python-programming-exercises

100+ Python challenging programming exercises

remove_blocks_from_aln

roary

Rapid large-scale prokaryote pan genome analysis

sequence-search-tool-for-antimicrobial-resistance-sstar-

Antimicrobial resistance gene predictor

sisrs

Site Identification from Short Read Sequences.

snp-sites

Finds SNP sites from a multi-FASTA alignment file

srst2

Short Read Sequence Typing for Bacterial Pathogens

vcflib

a simple C++ library for parsing and manipulating VCF files, + many command-line utilities