bhattlab's repositories
kraken2_classification
Snakemake workflow for metagenomic classification with Kraken2
bhattlab_workflows
Computational workflows for metagenomics tasks, by the Bhatt lab
StrainSifter
A straightforward bioinformatic pipeline for detecting a bacterial strain in one or more metagenome(s).
SmORFinder
A command line tool to identify and annotate small proteins in microbial sequencing datasets.
metagenomics_workflows
Workflows for metagenomic sequence data processing and analysis.
AWIGen2Microbiome
Repository for the AWI-Gen 2 microbiome project workflows, analysis, and results.
Benchmarking
Repository for 2021 sample stability benchmarking data analysis and figures
SupplementaryInformation
Supplementary information for some of our lab's publications.
absolute-abundance-16s
absolute abundance calculations from 16S rRNA qPCR or ddPCR
BacMetSearch
A command line tool to perform local DIAMOND searches against the BacMet database.
bhattlab_workflows_nf
Computational workflows for metagenomics tasks, packaged with Nextflow and Singularity.
DeepKingNet
A command line tool to classify nucleotide sequences as prokaryotic or eukaryotic.
hmmetariboseq
HMM for Metaribosq
MGEfinder-singularity
A singularity image for the MGEfinder software