cedwardson4

cedwardson4's Stars

• steineggerlab/foldseek

  Foldseek enables fast and sensitive comparisons of large structure sets.

  Language:C757101

• rcedgar/usearch12

  Open-source usearch

  Language:C++697

• nf-core/mag

  Assembly and binning of metagenomes

  Language:Nextflow199103

• twbattaglia/MicrobeDS

  A repository for large-scale microbiome datasets, formatted for phyloseq

  Language:R305

• wwood/galah

  More scalable dereplication for metagenome assembled genomes

  Language:Rust4510

• escamero/mirlyn

  Language:R113

• alexcritschristoph/RPxSuite

  Identifies and clusters marker genes to delineate species groups in metagenomes

  Language:Python5

• rotheconrad/bacterial_strain_definition

  Contains the code and workflow for the bacterial strain definition paper with Kostas Kostantinidis

  Language:Python8

• shendurelab/MIPGEN

  One stop MIP design and analysis

  Language:C++2219

• 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

  Language:Jupyter Notebook64

• quadram-institute-bioscience/namingGTDB

  Language:Python21

• 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.

  Language:Shell4

• bluenote-1577/sylph

  ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.

  Language:Rust1316

• mourisl/centrifuger

  Classifier for metagenomic sequences using FM-index with run-block compressed BWT.

  Language:C++393

• shenwei356/taxonkit

  A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

  Language:Go36529

• Chartiza/Microbiome

  scripts for microbiome analysis

  Language:HTML112

• jolespin/veba

  A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes

  Language:Python749

• ProbstLab/uBin

  Language:TypeScript191

• chklovski/CheckM2

  Assessing the quality of metagenome-derived genome bins using machine learning

  Language:Scilab16219

• FrederickHuangLin/ANCOMBC

  Differential abundance (DA) and correlation analyses for microbial absolute abundance data

  Language:R10326

• vinisalazar/metaphor

  Metaphor: a general-purpose workflow for assembly and binning of metagenomes

  Language:Python373

• dr-joe-wirth/phantasm

  PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes

  Language:Python21

• BigDataBiology/SemiBin

  SemiBin: metagenomics binning with self-supervised deep learning

  Language:Python11110

• biobakery/MetaPhlAn

  MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

  Language:Python28883

• fulcrumgenomics/fgbio

  Tools for working with genomic and high throughput sequencing data.

  Language:Scala30867

• cmdcolin/oddgenes

  A small database of weird gene annotations

  Language:Perl19811

• mdsufz/MuDoGeR

  MuDoGeR makes the recovery of genomes from prokaryotes, viruses, and eukaryotes from metagenomes easy.

  Language:Shell8610

• 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

  Language:Perl102

• KIT-IBG-5/mdmcleaner

  MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs

  Language:Python186

• thackl/gggenomes

  A grammar of graphics for comparative genomics

  Language:R58064