Alternatives and similar repositories for kraken

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

• DaehwanKimLab / centrifuge
  Classifier for metagenomic sequences
  ☆266Updated 3 months ago
• roblanf / minion_qc
  Quality control for MinION sequencing data
  ☆216Updated 2 years ago
• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆247Updated last year
• fbreitwieser / krakenuniq
  🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
  ☆239Updated last year
• sanger-pathogens / snp-sites
  Finds SNP sites from a multi-FASTA alignment file
  ☆266Updated 4 years ago
• wdecoster / nanopack
  An overview of all nanopack tools
  ☆268Updated 2 years ago
• arq5x / poretools
  a toolkit for working with Oxford nanopore data
  ☆245Updated 2 years ago
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆332Updated 2 weeks ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆241Updated 4 years ago
• isovic / racon
  Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr…
  ☆289Updated last year
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆368Updated 3 years ago
• wdecoster / nanofilt
  Filtering and trimming of long read sequencing data
  ☆209Updated 2 years ago
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆145Updated 10 years ago
• bioinformatics-centre / kaiju
  Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
  ☆290Updated 5 months ago
• philres / ngmlr
  NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on r…
  ☆306Updated last year
• ndierckx / NOVOPlasty
  NOVOPlasty - The organelle assembler and heteroplasmy caller
  ☆191Updated last year
• tseemann / barrnap
  Bacterial ribosomal RNA predictor
  ☆255Updated 2 years ago
• loneknightpy / idba
  ☆131Updated 2 years ago
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆283Updated 11 months ago
• DRL / blobtools
  Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
  ☆204Updated last year
• jenniferlu717 / Bracken
  Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…
  ☆321Updated 7 months ago
• artic-network / artic-ncov2019
  ARTIC nanopore protocol for nCoV2019 novel coronavirus
  ☆170Updated 2 years ago
• tseemann / shovill
  ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
  ☆236Updated 2 years ago
• rrwick / Filtlong
  quality filtering tool for long reads
  ☆365Updated last week
• najoshi / sickle
  Windowed Adaptive Trimming for fastq files using quality
  ☆223Updated 8 years ago
• alekseyzimin / masurca
  ☆261Updated 3 months ago
• KamilSJaron / smudgeplot
  Inference of ploidy and heterozygosity structure using whole genome sequencing data
  ☆277Updated 3 weeks ago
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆320Updated 5 months ago
• malonge / RaGOO
  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
  ☆172Updated 4 years ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆214Updated last year