metAMOS - assembly and analysis pipeline for metagenomic data.
VALET - de novo validation pipeline for metagenomic assembles.
MaryGold - software for graph-based analysis of genomic variation within metagenomic assemblies.
Bambus 2 - scaffolder for metagenomic data. Explicitly accounts for and detects genomic variants.
MetagenomeSeq - statistical package for differential abundance in metagenomic case/control studies. Relies on a linear model framework and includes a zero-inflated component to handle sparsity.
Metastats - statistical package for differential abundance in metagenomic case/control studies based on non-parametric t-test.
AMOS - Modular, open-source framework for developing assembly algorithms. Among the programs developed within the AMOS framework are:
AMOScmp - comparative sequence assembler. AMOScmp was used in a study that identified the presence of the bacterial endosymbiont Wolbachia within several fruit fly genomes (see paper).
Minimus - streamlined assembly program developed specifically for small assembly tasks (single genes, BACs, viral genomes). Minimus is being used to assemble a collection of strains of the flu virus (see project website). Also, an extension (Minimus-SR) was written to handle short-read sequencing data.
Bambus - the first publicly-available standalone scaffolding program.
Figaro - "blind" vector trimming software
SOMA - scaffolder for optical maps
DYIG (do it yourself genomics) Bacterial genome annotation pipeline
454-Sanger hybrid assembler
Bowtie - fast aligner based on Burrows-Wheeler transform
Minimus-SR - Version of minimus that works with short reads.
DYIG (do it yourself genomics) Bacterial genome annotation pipeline
ARDB - Antibiotic resistance factors in bacteria
Conserved genomic elements in bacteria (in progress)