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482

other

17

Quickly search, compare, and analyze genomic and metagenomic data sets.

kmer rust python minhash sourmash sketching fracminhash hacktoberfest bioinformatics scaled-minhash taxonomic-profiling taxonomic-classification

Created 2016-04-09

2,094 commits to latest branch, last one a day ago

kaiju bioinformatics-centre

67

273

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 4 months ago

sylph bluenote-1577

7

200

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

273 commits to main branch, last one 8 days ago

ampliseq nf-core

122

189

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 about a month ago

kmcp shenwei356

13

181

mit

6

Accurate metagenomic profiling && Fast large-scale sequence/genome searching

cobs kmer bigsi sketch virome syncmers searching sketching fracminhash metagenomics scaled-minhash taxonomic-profiling taxonomic-classification

Created 2020-10-30

522 commits to main branch, last one about a year ago

taxprofiler nf-core

37

132

mit

155

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

nf-core shotgun illumina nanopore nextflow pathogen pipeline workflow profiling long-reads microbiome metagenomics bioinformatics classification taxonomic-profiling taxonomic-classification

Created 2022-02-18

2,031 commits to master branch, last one 23 days ago

Metabuli steineggerlab

10

123

gpl-3.0

6

Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.

k-mer taxonomy metagenomics bioinformatics taxonomic-classification

Created 2020-09-09

3,053 commits to master branch, last one 2 months ago

epa-ng pierrebarbera

7

79

agpl-3.0

12

Massively parallel phylogenetic placement of genetic sequences

mpi mpi-io openmp placement phylogenetics bioinformatics taxonomic-classification

Created 2015-11-03

821 commits to master branch, last one 2 years ago

flextaxd FOI-Bioinformatics

8

65

gpl-3.0

3

FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )

16s gtdb ganon kraken2 amplicon centrifuge krakenuniq ncbi-database ncbi-taxonomy custom-database custom-taxonomy taxonomic-classification taxonomic-classifications metagenomic-classification

Created 2019-06-20

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

vclust refresh-bio

1

53

gpl-3.0

3

Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes

viruses clustering dereplication bacteriophages genome-sequence sequence-similarity taxonomic-classification average-nucleotide-identity

Created 2023-08-30

47 commits to main branch, last one a day ago

kraken-biom smdabdoub

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50

mit

3

Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).

kraken taxonomy biom-format metagenomics bioinformatics taxonomic-classification

Created 2016-04-15

57 commits to master branch, last one 2 years ago

Taxor JensUweUlrich

2

43

bsd-3-clause

2

Fast and space-efficient taxonomic classification of long reads

kmer bioinf refseq syncmer taxonomy long-read microbiome xor-filter em-algorithm metagenomics bioinformatics pseudo-alignment taxonomic-profiling long-read-sequencing interleaved-xor-filter taxonomic-classification

Created 2022-01-05

103 commits to main branch, last one about a month ago