raufs
Interested in using and developing bioinformatics tools to understand microbial evolution & ecology
Madison, WI
Pinned Repositories
ConSequences
Suite to delineate contiguous and conserved sequences from assemblies and search for their presence in raw sequencing data.
seQuoia
A framework for diverse omics workflows, primarily focused on QC, processing and analysis of bacterial genomic sequencing sets.
codoff
codoff: a program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, phage, etc.) relative to the full genome.
lsaBGC-Pan
lsaBGC - suite for pan-BGC-omics analysis
zol
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
Admixture
BiG-MAP
bioconda-recipes
Conda recipes for the bioconda channel.
codoff
codoff: a program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, phage, etc.) relative to the full genome.
skDER
skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and metagenomics.
raufs's Repositories
raufs/skDER
skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and metagenomics.
raufs/BiG-MAP
raufs/Admixture
raufs/bioconda-recipes
Conda recipes for the bioconda channel.
raufs/codoff
codoff: a program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, phage, etc.) relative to the full genome.
raufs/ConSequences
Suite to delineate contiguous and conserved sequences from assemblies and search for their presence in raw sequencing data.
raufs/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
raufs/lsaBGC
lsaBGC - Lineage Specific Analysis of Biosynthetic Gene Clusters
raufs/minima
Minima is a one-size-fits-all Jekyll theme for writers.
raufs/gtdb_gca_to_taxa_mappings
Directory with GTDB GCA accession to taxonomy mappings used by various programs.
raufs/OrthoFinder
Phylogenetic orthology inference for comparative genomics
raufs/PerMutation
Code and programs developed for Tn-Seq analysis of E. faecalis MMH594.
raufs/personal-website
raufs/raufs
raufs/raufs.github.io
raufs/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.
raufs/seQuoia
A framework for diverse omics workflows, primarily focused on QC, processing and analysis of bacterial genomic sequencing sets.
raufs/zol