Alternatives and similar repositories for krakenuniq

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

• DaehwanKimLab / centrifuge
  Classifier for metagenomic sequences
  ☆267Updated 5 months ago
• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆248Updated last year
• DRL / blobtools
  Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
  ☆208Updated last year
• wdecoster / chopper
  ☆218Updated 3 weeks ago
• PacificBiosciences / pb-metagenomics-tools
  Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics
  ☆195Updated 2 months ago
• wdecoster / nanofilt
  Filtering and trimming of long read sequencing data
  ☆209Updated 2 years ago
• neherlab / pan-genome-analysis
  Processing pipeline for pan-genome visulization and exploration
  ☆142Updated 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…
  ☆284Updated last year
• rrwick / Long-read-assembler-comparison
  Benchmarking of long-read assembly tools for bacterial whole genomes
  ☆172Updated 4 years ago
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆334Updated 2 months ago
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆329Updated 7 months ago
• Nextomics / NextPolish
  Fast and accurately polish the genome generated by long reads.
  ☆236Updated 10 months ago
• tseemann / barrnap
  Bacterial ribosomal RNA predictor
  ☆259Updated 2 years ago
• mahulchak / quickmerge
  A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.
  ☆205Updated 3 years ago
• aineniamh / snipit
  snipit: summarise snps relative to your reference sequence
  ☆162Updated 2 months ago
• MGXlab / CAT_pack
  CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metage…
  ☆223Updated last month
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆279Updated 3 months ago
• roblanf / minion_qc
  Quality control for MinION sequencing data
  ☆217Updated 2 years ago
• rrwick / Deepbinner
  a signal-level demultiplexer for Oxford Nanopore reads
  ☆126Updated 4 years ago
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆142Updated 3 months ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆283Updated 9 months ago
• tseemann / any2fasta
  Convert various sequence formats to FASTA
  ☆139Updated 3 years ago
• yfukasawa / LongQC
  LongQC is a tool for the data quality control of the PacBio and ONT long reads.
  ☆176Updated last year
• KamilSJaron / smudgeplot
  Inference of ploidy and heterozygosity structure using whole genome sequencing data
  ☆281Updated this week
• nf-core / taxprofiler
  Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
  ☆169Updated this week
• schatzlab / genomescope
  Fast genome analysis from unassembled short reads
  ☆299Updated last year
• OpenGene / fastplong
  Ultra-fast preprocessing and quality control for long-read sequencing data
  ☆195Updated 2 months ago
• CAMI-challenge / CAMISIM
  CAMISIM: Simulating metagenomes and microbial communities
  ☆218Updated last week
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆282Updated 2 weeks ago
• artic-network / artic-ncov2019
  ARTIC nanopore protocol for nCoV2019 novel coronavirus
  ☆170Updated 2 years ago