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GenomeTools is a collection of algorithms to manipulate genomics related file format. The primary purpose is to convert file formats from one to another.
High-throughput *NA sequencing quality control
Graph genome browser
Digital spoligotyping of MTB strains from Illumina read data
Abeel Toolkit is set of utility classes that are used in our other projects.
ProSOM is a promoter prediction program based on unsupervised clustering of physical properties of DNA. The program can clearly distinguish between the structural profiles of promoter sequences and other genomic sequences by using self-organizing maps.
Macaw is a tool to lineage-type MTB samples and to identified strain mixes in WGS data sets.
A tool to generate synthetic aneuploid and polyploid genomes
peacock is a visualization library for generating vector graphics from (very) large phylogenies and many types of meta-data
Approximate tree building with kmers
Supplementary data for our CENPK113-7D assembly paper
Haplotype-aware de novo genome assembly for polyploid organisms from long read data
Multi-reference genome browser
Snakemake pipeline for the PHASM genome assembler
PEDCA is a ploidy estimation algorithm that infers copy number of the contigs submitted as input based on the read coverage that are aligned to them. It only requires as an input an alignment file in .bam or .sam format of a library or set of libraries aligned to a reference file of the contigs that will be estimated.
Java Machine Learning Library
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
IS6110 discovery from NGS data
Order and orient
Rapid TB drug resistance determination from NGS data
Emu is a tool that canonicalizes non-identical representations of large insertions and deletions (indels) and substitutions across multiple genome samples.
Pilon is an automated genome assembly improvement and variant detection tool