Alternatives and similar repositories for centrifuge:

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

• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆70Updated 3 years ago
• SegataLab / panphlan
  PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
  ☆45Updated last year
• fanglab / mbin
  mBin: a methylation-based binning framework for metagenomic SMRT sequencing reads
  ☆25Updated 2 years ago
• genomeannotation / GAG
  Generates an NCBI .tbl file of annotations on a genome.
  ☆66Updated 7 years ago
• rrwick / Metagenomics-Index-Correction
  ☆81Updated last year
• nanoporetech / pipeline-umi-amplicon
  Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers
  ☆33Updated last year
• bvalot / pyMLST
  whole genome MLST analysis
  ☆41Updated this week
• ddarriba / prottest3
  Automatically exported from code.google.com/p/prottest3
  ☆36Updated 7 years ago
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆40Updated 4 years ago
• sanger-pathogens / assembly_improvement
  Improve the quality of a denovo assembly by scaffolding and gap filling
  ☆56Updated 4 years ago
• B-UMMI / long-read-catalog
  catalog for long-read sequencing tools
  ☆32Updated 2 years ago
• jhawkey / IS_mapper
  IS mapping software
  ☆53Updated 3 years ago
• dwinter / pafr
  Read, manipulate and visualize 'Pairwise mApping Format' data in R
  ☆71Updated 3 years ago
• metagenomics / denbi-nanopore-training
  de.NBI Nanopore Training Course
  ☆20Updated 2 years ago
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆58Updated last year
• marbl / harvest
  ☆52Updated 3 years ago
• Finn-Lab / MGS-gut
  Analysing Metagenomic Species (MGS)
  ☆41Updated 4 years ago
• wdecoster / nanolyse
  Remove lambda phage reads from a fastq file
  ☆29Updated 2 years ago
• fbreitwieser / bamcov
  Quickly calculate and visualize sequence coverage in alignment files
  ☆99Updated 5 years ago
• oschwengers / asap
  A scalable bacterial genome assembly, annotation and analysis pipeline
  ☆73Updated last year
• rhysf / Synima
  Synteny Imager
  ☆61Updated 7 months ago
• DeniRibicic / q2ONT
  Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2
  ☆29Updated 5 years ago
• segalab / SGVFinder
  ☆32Updated last year
• thackl / minidot
  Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2
  ☆74Updated 8 years ago
• sirselim / guppy_parameter_optimiser
  A small bash script that automates sweeping Guppy parameters in an attempt to optimise basecalling rate
  ☆30Updated 2 years ago
• Serka-M / Digester-MultiSequencing
  Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing
  ☆21Updated 2 years ago
• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆71Updated 5 years ago
• nanoporetech / ont_tutorial_basicqc
  A bioinformatics tutorial demonstrating a best-practice workflow to review a flowcell's sequence_summary.txt
  ☆30Updated 4 years ago
• xiaoli-dong / metaerg
  ☆41Updated 4 years ago
• elimoss / metagenomics_workflows
  Workflows for metagenomic sequence data processing and analysis.
  ☆17Updated 5 years ago