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Variational autoencoder for metagenomic binning
Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
Fast and accurate de novo assembler for long reads
Horizontal gene transfer (HGT) identification pipeline
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Official code repository for GATK versions 4 and up
MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
The stairway plot is a method for inferring detailed population demographic history using the site frequency spectrum (SFS) from DNA sequence data.
Software for painlessly estimating average nucleotide diversity within and between populations
Scripts for analysis used during the course
Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style SFS for demographic analysis
Tutorials on phylogenetic and phylogenomic inference
Visualization and analysis software for Hi-C data -
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Python library to handle Gene Ontology (GO) terms
PANAM2 is a pipeline for depicting the microbial community by implementing a phylogenetic approach for the annotation of the gene coding for 16S and 18S rRNA. It is based on PANAM (Taib et al. 2013…
a long-read error correction tool using the multi-string Burrows Wheeler Transform
Ultra-fast de novo assembler using long noisy reads
Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
Pilon is an automated genome assembly improvement and variant detection tool
A single molecule sequence assembler for genomes large and small.