cedwardson4
Microbiologist at Taconic Biosciences, former postdoc at Shedd Aquarium, PhD from University of Georgia
Albany, NY, USA
cedwardson4's Stars
steineggerlab/foldseek
Foldseek enables fast and sensitive comparisons of large structure sets.
rcedgar/usearch12
Open-source usearch
nf-core/mag
Assembly and binning of metagenomes
twbattaglia/MicrobeDS
A repository for large-scale microbiome datasets, formatted for phyloseq
wwood/galah
More scalable dereplication for metagenome assembled genomes
escamero/mirlyn
alexcritschristoph/RPxSuite
Identifies and clusters marker genes to delineate species groups in metagenomes
rotheconrad/bacterial_strain_definition
Contains the code and workflow for the bacterial strain definition paper with Kostas Kostantinidis
shendurelab/MIPGEN
One stop MIP design and analysis
flannsmith/metaphlan-plot-by-taxa
Python script to convert the metagenomic profile txt file to taxa level plots in python's bokeh and R's phyloseq
quadram-institute-bioscience/namingGTDB
BenBeresfordJones/MGBC-Toolkit
Toolkit for identifying the closest taxonomically and functionally related species between the human and mouse gut microbiotas, as well as the taxonomic locations of functions of interest between hosts.
bluenote-1577/sylph
ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.
mourisl/centrifuger
Classifier for metagenomic sequences using FM-index with run-block compressed BWT.
shenwei356/taxonkit
A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
Chartiza/Microbiome
scripts for microbiome analysis
jolespin/veba
A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes
ProbstLab/uBin
chklovski/CheckM2
Assessing the quality of metagenome-derived genome bins using machine learning
FrederickHuangLin/ANCOMBC
Differential abundance (DA) and correlation analyses for microbial absolute abundance data
vinisalazar/metaphor
Metaphor: a general-purpose workflow for assembly and binning of metagenomes
dr-joe-wirth/phantasm
PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes
BigDataBiology/SemiBin
SemiBin: metagenomics binning with self-supervised deep learning
biobakery/MetaPhlAn
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
fulcrumgenomics/fgbio
Tools for working with genomic and high throughput sequencing data.
cmdcolin/oddgenes
A small database of weird gene annotations
mdsufz/MuDoGeR
MuDoGeR makes the recovery of genomes from prokaryotes, viruses, and eukaryotes from metagenomes easy.
TSTanabe/HMSSS
HMS-S-S: a tool for the identification of sulfur metabolism-related genes and analysis of operon structures in genome and metagenome assemblies
KIT-IBG-5/mdmcleaner
MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs
thackl/gggenomes
A grammar of graphics for comparative genomics