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admixture

big-map

bioconda-recipes

Conda recipes for the bioconda channel.

consequences

Suite to delineate contiguous and conserved sequences from assemblies and search for their presence in raw sequencing data.

genomes-mags-database

Creation of a database of Genbank genomes including isolate reference genomes and MAGs, and parallelizing 1000s of genome searches for a specific marker

gtdb_gca_to_taxa_mappings

Directory with GTDB GCA accession to taxonomy mappings used by various programs.

lsabgc

lsaBGC - Lineage Specific Analysis of Biosynthetic Gene Clusters

minima

Minima is a one-size-fits-all Jekyll theme for writers.

orthofinder

Phylogenetic orthology inference for comparative genomics

permutation

Code and programs developed for Tn-Seq analysis of E. faecalis MMH594.

personal-website

raufs

raufs.github.io

rotation-in-anantharaman-lab

Programs developed for rotation in the Anantharaman lab, includes MetaDownSampler.py - which takes in a metagenome assembly and a BAM file containing self/reflexive alignment of reads to the assemblies to realistically simulate fragmentation of metagenome assembly if sequencing depth was lowered.

sequoia

A framework for diverse omics workflows, primarily focused on QC, processing and analysis of bacterial genomic sequencing sets.

skder

skDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and metagenomics.

zol