taxonomic-profiling

There are 0 repository under taxonomic-profiling topic.

sourmash
sourmash-bio / sourmash
Quickly search, compare, and analyze genomic and metagenomic data sets.
minhash bioinformatics rust python sourmash fracminhash scaled-minhash kmer sketching taxonomic-classification taxonomic-profiling hacktoberfest
Language:Python 522
nf-core / ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
amplicon-sequencing 16s nf-core nextflow pipeline workflow metagenomics rrna 18s its metabarcoding qiime2 edna taxonomic-classification illumina iontorrent microbiome pacbio taxonomic-profiling
Language:Nextflow 197
kmcp
shenwei356 / kmcp
Accurate metagenomic profiling && Fast large-scale sequence/genome searching
kmer sketch searching metagenomics taxonomic-classification taxonomic-profiling scaled-minhash syncmers cobs sketching bigsi fracminhash virome
Language:Go 196
nf-core / taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
bioinformatics classification illumina long-reads metagenomics microbiome nanopore nextflow nf-core pathogen pipeline profiling shotgun taxonomic-classification taxonomic-profiling workflow
Language:Nextflow 142
JensUweUlrich / Taxor
Fast and space-efficient taxonomic classification of long reads
kmer long-read long-read-sequencing metagenomics syncmer taxonomic-classification taxonomic-profiling bioinf em-algorithm pseudo-alignment xor-filter interleaved-xor-filter bioinformatics microbiome refseq taxonomy
Language:C++ 43
taxpasta
taxprofiler / taxpasta
TAXnomic Profile Aggregation and STAndardisation
metagenomics python standardisation bioinformatics profiling classification metagenomic-classification taxonomic-classifications taxonomic-profiling
Language:Python 39
xinehc / melon
Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
metagenomics taxonomic-profiling long-read-sequencing
Language:Python 33
treangenlab / lemur
Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets
long-read-sequencing long-reads metagenomic-analysis metagenomic-classification metagenomics taxonomic-classification taxonomic-profiling
Language:Python 24
meteor
metagenopolis / meteor
Meteor is a plateform for quantitative metagenomics profiling of complex ecosystems. Meteor relies on genes catalogue to perform species-level taxonomic profiling (Bacteria, Archaea and Eukaryotes), functional analysis and strain-level population structure inference.
metagenomics strain-profiling taxonomic-profiling functionnal-profiling
Language:Python 20
nf-core / detaxizer
A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.
nextflow nf-core pipeline workflow de-identification decontamination edna fastq filter long-reads metabarcoding metagenomics microbiome nanopore short-reads shotgun taxonomic-classification taxonomic-profiling
Language:Nextflow 18
PROBIC / mSWEEP
mSWEEP High-resolution sweep metagenomics using fast probabilistic inference
plate-sweep metagenomics taxonomic-profiling high-throughput-sequencing c-plus-plus
Language:C++ 14
nf-core / createtaxdb
Parallelised and automated construction of metagenomic classifier databases of different tools
database database-builder metagenomic-profiling metagenomics nextflow nf-core pipeline profiling taxonomic-profiling workflow
Language:Nextflow 9
DavideScarpetta / taxonomic_profiling
Metabarcoding analysis pipeline, using DADA2 and qiime2
bioinformatics bioinformatics-pipeline cutadapt dada2 metabarcoding metabarcoding-data qiime2 taxonomic-profiling
Language:Shell 0
hermidalc / dragonfish
A fast, efficient, and accurate functional and taxonomic meta-omic profiler built on Pufferfish and the ccdBG
functional-profiling metagenomic-analysis metagenomic-pipeline metagenomics metatranscriptomic-analysis metatranscriptomic-pipeline metatranscriptomics microbiome-analysis microbiome-workflow taxonomic-classification taxonomic-profiling
Language:Python 0