Search Results - RepositoryStats

MMseqs2 soedinglab

197

1.5k

mit

32

MMseqs2: ultra fast and sensitive search and clustering suite

blast mmseqs linclust taxonomy alignment metagenomics bioinformatics profile-search sequence-search sequence-clustering

Created 2016-07-20

6,464 commits to master branch, last one 19 hours ago

vsearch torognes

125

671

other

43

Versatile open-source tool for microbiome analysis

fasta fastq search chimera amplicon clustering microbiome metagenomics metabarcoding bioinformatics sequence-alignment

Created 2014-05-16

3,288 commits to master branch, last one 4 days ago

megahit voutcn

135

610

gpl-3.0

37

Ultra-fast and memory-efficient (meta-)genome assembler

genomics succinct metagenomics bioinformatics data-structures genome-assembly

Created 2014-09-25

693 commits to master branch, last one about a year ago

GTDBTk Ecogenomics

82

479

gpl-3.0

23

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

archaea bacteria taxonomy metagenomics nomenclature phylogenetics bioinformatics species-assignments

Created 2016-11-29

961 commits to master branch, last one 6 months ago

dada2 benjjneb

143

471

lgpl-3.0

39

Accurate sample inference from amplicon data with single nucleotide resolution

amplicon taxonomy microbiome bioconductor metagenomics metabarcoding bioinformatics

Created 2014-12-17

793 commits to master branch, last one 7 days ago

anvio merenlab

145

443

gpl-3.0

30

An analysis and visualization platform for 'omics data

anvio python science javascript pangenomics metagenomics phylogenomics visualization bioinformatics metatranscriptomics population-genetics comparative-genomics

Created 2014-02-26

19,416 commits to master branch, last one 2 days ago

SqueezeMeta jtamames

81

382

gpl-3.0

9

A complete pipeline for metagenomic analysis

pipeline metagenomes metagenomics taxonomic-assignment

Created 2018-03-15

1,303 commits to master branch, last one 8 days ago

atlas metagenome-atlas

99

377

bsd-3-clause

15

ATLAS - Three commands to start analyzing your metagenome data

assembly snakemake annotation metagenomics genomic-binning functional-annotation taxonomic-classifications

Created 2016-11-30

2,820 commits to main branch, last one 3 months ago

training-material galaxyproject

905

309

mit

53

A collection of Galaxy-related training material

ngs rnaseq chip-seq training tutorial materials usegalaxy proteomics metagenomics hacktoberfest

Created 2015-06-29

28,422 commits to main branch, last one 17 hours ago

MetaPhlAn biobakery

86

304

mit

20

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

tools public python biobakery metagenomics

Created 2020-02-20

836 commits to master branch, last one about a month ago

kaiju bioinformatics-centre

66

272

gpl-3.0

15

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

taxonomy metagenomics bioinformatics taxonomic-classification next-generation-sequencing

Created 2015-11-16

249 commits to master branch, last one 3 months ago

drep MrOlm

37

263

unknown

8

Rapid comparison and dereplication of genomes

assembly metagenomics microbiology bioinformatics microbial-genomes

Created 2016-09-27

274 commits to master branch, last one 7 days ago

DRAM WrightonLabCSU

52

256

gpl-3.0

6

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

genomics annotation microbiome metagenomics bioinformatics viral-genomics viral-metagenomics metagenome-assembled-genomes

Created 2019-02-11

867 commits to master branch, last one 18 days ago

krakenuniq fbreitwieser

43

224

gpl-3.0

16

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

metagenomics bioinformatics

Created 2017-11-11

550 commits to master branch, last one 11 months ago

biomartr ropensci

29

217

unknown

14

Genomic Data Retrieval with R

r genome rstats biomart genomics proteome r-package metagenomics ncbi-genbank meta-analysis peer-reviewed ensembl-servers genome-retrieval genome-annotation sequenced-genomes database-retrieval

Created 2014-08-05

2,415 commits to master branch, last one 4 months ago

mag nf-core

110

217

mit

161

Assembly and binning of metagenomes

binning nf-core assembly nanopore nextflow pipeline workflow annotation metagenomes metagenomics bioinformatics nanopore-sequencing long-read-sequencing

Created 2018-05-22

2,418 commits to master branch, last one 24 days ago

metaGEM franciscozorrilla

43

203

mit

5

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

mags snakemake metabolism microbiome metagenomics bioinformatics gut-microbiome systems-biology metabolic-models microbial-ecology metabolic-modeling computational-biology flux-balance-analysis genome-scale-metabolic-model metagenome-assembled-genomes

Created 2018-06-14

669 commits to master branch, last one 3 months ago

sylph bluenote-1577

7

191

mit

3

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

k-mer metagenomics sketching-algorithm taxonomic-classification average-nucleotide-identity

Created 2023-05-06

266 commits to main branch, last one 15 days ago

ampliseq nf-core

118

188

mit

152

Amplicon sequencing analysis workflow using DADA2 and QIIME2

16s 18s its edna rrna pacbio qiime2 nf-core illumina nextflow pipeline workflow iontorrent microbiome metagenomics metabarcoding amplicon-sequencing taxonomic-profiling taxonomic-classification

Created 2018-09-26

2,541 commits to master branch, last one 8 days ago