ekquaye

ekquaye's Stars

• Rostlab/EAT

  Embedding-based annotation transfer (EAT) uses Euclidean distance between vector representations (embeddings) of proteins to transfer annotations from a set of labeled lookup protein embeddings to query protein embedding.

  Language:Python287

• soedinglab/MMseqs2

  MMseqs2: ultra fast and sensitive search and clustering suite

  Language:C1.4k195

• weizhongli/cdhit

  Automatically exported from code.google.com/p/cdhit

  Language:Perl641129

• bacpop/CELEBRIMBOR

  Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs

  Language:Python22

• ncbi/pgap

  NCBI Prokaryotic Genome Annotation Pipeline

  Language:Common Workflow Language31390

• sanger-pathogens/Roary

  Rapid large-scale prokaryote pan genome analysis

  Language:Perl323190

• qiime2/qiime2

  Official repository for the QIIME 2 framework.

  Language:Python473240

• benjjneb/dada2

  Accurate sample inference from amplicon data with single nucleotide resolution

  Language:R470142

• eggnogdb/eggnog-mapper

  Fast genome-wide functional annotation through orthology assignment

  Language:Python568106

• tseemann/prokka

  :zap: :aquarius: Rapid prokaryotic genome annotation

  Language:Perl834226

• biobakery/shortbred

  ShortBRED is a pipeline to take a set of protein sequences, reduce them to a set of unique identifying strings ("markers"), and then search for these markers in metagenomic data and determine the presence and abundance of the protein families of interest.

  Language:Python285

• microbiome/microbiome

  microbiome R package

  Language:R28854

• vegandevs/vegan

  R package for community ecologists: popular ordination methods, ecological null models & diversity analysis

  Language:R45298

• bluenote-1577/skani

  Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.

  Language:Rust16910

• biobakery/anpan

  Language:R6

• biobakery/waafle

  http://huttenhower.sph.harvard.edu/waafle

  Language:Python41

• biobakery/metawibele

  MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome

  Language:Python203

• biobakery/Maaslin2

  MaAsLin2: Microbiome Multivariate Association with Linear Models

  Language:R11835

• biobakery/MMUPHin

  MMUPHin: Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies

  Language:R84

• oschwengers/bakta

  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

  Language:Python44254

• BenLangmead/bowtie2

  A fast and sensitive gapped read aligner

  Language:C++675159

• motu-tool/mOTUs

  motus - a tool for marker gene-based OTU (mOTU) profiling

  Language:Python14725

• bbuchfink/diamond

  Accelerated BLAST compatible local sequence aligner.

  Language:C++1.1k182

• stamatak/standard-RAxML

  Language:C329192

• iqtree/iqtree2

  NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org

  Language:C++24456

• Ecogenomics/GTDBTk

  GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

  Language:Python47682

• gtonkinhill/panaroo

  An updated pipeline for pangenome investigation

  Language:Python26934

• merenlab/anvio

  An analysis and visualization platform for 'omics data

  Language:Python440145

• chklovski/CheckM2

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

  Language:Scilab17020

• hyattpd/Prodigal

  Prodigal Gene Prediction Software

  Language:C44685