Alternatives and similar repositories for kraken2_classification

Users that are interested in kraken2_classification are comparing it to the libraries listed below

• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆59Updated last year
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆69Updated 4 years ago
• rrwick / Metagenomics-Index-Correction
  ☆84Updated 2 years ago
• mjsull / Easyfig
  Development version of Easyfig
  ☆102Updated last year
• smdabdoub / kraken-biom
  Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…
  ☆56Updated 3 years ago
• nf-core / bacass
  Simple bacterial assembly and annotation pipeline
  ☆79Updated last month
• DiltheyLab / MetaMaps
  Long-read metagenomic analysis
  ☆106Updated 2 years ago
• fanglab / nanodisco
  nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nano…
  ☆70Updated 3 years ago
• AstrobioMike / bit
  Bioinformatics Tools
  ☆89Updated last month
• FOI-Bioinformatics / flextaxd
  FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomi…
  ☆67Updated 8 months ago
• ignasrum / hocort
  HoCoRT - Remove specific organisms from sequencing reads
  ☆17Updated 10 months ago
• DeniRibicic / q2ONT
  Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2
  ☆29Updated 5 years ago
• PacificBiosciences / HiFi-16S-workflow
  Nextflow pipeline to analyze PacBio HiFi full-length 16S data
  ☆87Updated 4 months ago
• nmquijada / tormes
  Making whole bacterial genome sequencing data analysis easy
  ☆113Updated 6 months ago
• bjtully / BioData
  All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
  ☆79Updated 2 years ago
• lmrodriguezr / enveomics
  Scripts and libraries for Environmental Genomics
  ☆38Updated 9 months ago
• Mykrobe-tools / mykrobe
  Antibiotic resistance prediction in minutes
  ☆112Updated 11 months ago
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆55Updated 6 months ago
• donovan-h-parks / CompareM
  A toolbox for comparative genomics.
  ☆106Updated 4 years ago
• SegataLab / panphlan
  PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
  ☆46Updated 2 years ago
• UCSC-LoweLab / tRNAscan-SE
  A program for detection of tRNA genes
  ☆73Updated 3 years ago
• bhattlab / MGEfinder
  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
  ☆124Updated 2 years ago
• segalab / SGVFinder
  ☆32Updated 2 years ago
• Finn-Lab / MAG_Snakemake_wf
  Recovery of prokaryotic genomes from shotgun metagenomic sequencing data
  ☆62Updated 4 years ago
• chasewnelson / SNPGenie
  Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
  ☆118Updated 2 years ago
• SorenKarst / longread_umi
  ☆79Updated 5 years ago
• arumugamlab / msamtools
  Metagenomics-related extended functionalities to samtools
  ☆22Updated 2 years ago
• aleimba / bac-genomics-scripts
  Collection of scripts for bacterial genomics
  ☆49Updated 5 years ago
• vrmarcelino / CCMetagen
  Microbiome classification pipeline
  ☆65Updated 6 months ago
• happykhan / BRIG
  BRIG is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a f…
  ☆37Updated 6 years ago