kraken2 | Topic | Ecosyste.ms: Repos

Topic: "kraken2"

eric9n/Kun-peng

Kun-peng: an ultra-fast, low-memory footprint and accurate taxonomy classifier for all

Language: Rust - Size: 3.12 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 124 - Forks: 11

FOI-Bioinformatics/flextaxd

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

Language: Python - Size: 1.06 MB - Last synced at: 15 days ago - Pushed at: 3 months ago - Stars: 65 - Forks: 8

nf-core/hgtseq

A pipeline to investigate horizontal gene transfer from NGS data

Language: Nextflow - Size: 5.11 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 25 - Forks: 7

angelovangel/nxf-kraken2

A simple nextflow pipeline for running kraken2 and bracken in a docker container

Language: Nextflow - Size: 112 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 17 - Forks: 8

Ivarz/Conifer

Calculate confidence scores from Kraken2 output

Language: C - Size: 396 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 14 - Forks: 7

acvill/bracken_plot

A Shiny app for taxonomic abundance visualization

Language: R - Size: 356 KB - Last synced at: about 2 months ago - Pushed at: about 1 year ago - Stars: 7 - Forks: 1

pfeiferd/genestrip

Genestrip - Efficient read classification, filtering and k-mer counting for selected groups of species

Language: Java - Size: 94.8 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 6 - Forks: 0

iliapopov17/The-shadow-of-HIV

Repository for course project in Bioinformatics Institute 2023-2024

Language: Jupyter Notebook - Size: 32 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 3 - Forks: 1

ksumngs/v-met

A bare-bones, ridiculously simple metagenomics pipeline for viruses using Kraken 2 written in Nextflow.

Language: Nextflow - Size: 3.56 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 1

PopovIILab/KrakenParser

🗂️Parse multiple Kraken2 reports into CSV files on 6 taxonomical levels

Language: Shell - Size: 5.36 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 1 - Forks: 0

PopovIILab/BatShotMetaFlow

🦇🧫📊Study on bat gut shotgun metagenomics

Language: Jupyter Notebook - Size: 8.37 MB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 1 - Forks: 1

OpenOmics/weave

An awesome BCL demultiplexing and FastQ quality-control pipeline

Language: Python - Size: 1.5 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

Zheludev/KrakenGrafter

a simple python script for "grafting" on novel sequences to a custom Kraken2 database

Language: Python - Size: 45.9 KB - Last synced at: almost 2 years ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0

Royal-Botanic-Gardens-Victoria/PAFTOL-taxonomy-classifier

#Scripts to create Kraken2 database of PAFTOL V2.0 Angio353 genes. An excellent database for taxonomic identification of plants. #https://treeoflife.kew.org/ #https://github.com/DerrickWood/kraken2/wiki #Prior to using this script, download and install kraken2 and make sure it is working and in your PATH. #Make sure the location of the python scripts used below are also in your PATH #Download PAFTOL V2.0 Angio353 genes from Kew #After building the DB, the scripts kraken2paired.py and top_taxa.py can be used to identify taxonomy of unknown samples. #e.g. #kraken2paired.py "reads/*.fastq" kraken_results/ 0 24 kraken2_paftol2/ #top_taxa.py "kraken_results/*" kraken.out

Language: Python - Size: 11.7 KB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0