yatisht / usher

Related projects ⓘ

Alternatives and complementary repositories for usher

• connor-lab / ncov2019-artic-nf
  A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), wit…
  ☆90Updated last year
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆108Updated 6 months ago
• artic-network / fieldbioinformatics
  The ARTIC field bioinformatics pipeline
  ☆116Updated this week
• pierrebarbera / epa-ng
  Massively parallel phylogenetic placement of genetic sequences
  ☆78Updated 2 years ago
• jameshadfield / phandango
  an interactive viewer for populations of bacterial genomes linked by a phylogeny
  ☆117Updated 9 months ago
• tseemann / snp-dists
  Pairwise SNP distance matrix from a FASTA sequence alignment
  ☆127Updated 8 months ago
• aineniamh / snipit
  snipit: summarise snps relative to your reference sequence
  ☆149Updated last week
• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆54Updated 2 months ago
• medvedevgroup / SibeliaZ
  A fast whole-genome aligner based on de Bruijn graphs
  ☆141Updated 2 years ago
• rrwick / Polypolish
  a short-read polishing tool for long-read assemblies
  ☆145Updated 5 months ago
• lh3 / pangene
  Constructing a pangenome gene graph
  ☆174Updated 4 months ago
• lskatz / mashtree
  Create a tree using Mash distances
  ☆156Updated last year
• ncbi / SKESA
  SKESA assembler
  ☆112Updated last month
• epi2me-labs / wf-artic
  ARTIC SARS-CoV-2 workflow and reporting
  ☆49Updated 2 months ago
• AdmiralenOla / Scoary
  Pan-genome wide association studies
  ☆150Updated 5 months ago
• neherlab / pangraph
  A bioinformatic toolkit to align genome assemblies into pangenome graphs
  ☆90Updated 3 weeks ago
• eead-csic-compbio / get_homologues
  GET_HOMOLOGUES: a versatile software package for pan-genome analysis
  ☆110Updated last week
• conchoecia / odp
  oxford dot plots
  ☆136Updated last month
• glennhickey / progressiveCactus
  Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
  ☆83Updated 6 years ago
• andersen-lab / ivar
  iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
  ☆118Updated last month
• vgl-hub / gfastats
  A single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulatio…
  ☆92Updated 2 weeks ago
• soedinglab / metaeuk
  MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
  ☆178Updated 4 months ago
• nickjcroucher / gubbins
  Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
  ☆175Updated last week
• nf-core / viralrecon
  Assembly and intrahost/low-frequency variant calling for viral samples
  ☆125Updated 2 weeks ago
• marbl / parsnp
  Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can b…
  ☆129Updated this week
• waveygang / wfmash
  base-accurate DNA sequence alignments using WFA and mashmap3
  ☆177Updated this week
• Mykrobe-tools / mykrobe
  Antibiotic resistance prediction in minutes
  ☆106Updated this week
• gatech-genemark / ProtHint
  Protein hint generation pipeline for gene finding in eukaryotic genomes
  ☆57Updated last year
• SionBayliss / PIRATE
  A toolbox for pangenome analysis and threshold evaluation.
  ☆91Updated 2 years ago
• wdecoster / nanocomp
  Comparison of multiple long read datasets
  ☆108Updated 2 weeks ago