Alternatives and similar repositories for shusher

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

• althonos / pyskani
  PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.
  ☆27Updated 3 months ago
• piyuranjan / SNIKT
  Sequence-independent identification and removal of adapters/systemic contamination in shotgun sequencing data. https://doi.org/10.1093/bi…
  ☆18Updated 2 years ago
• salzberg-lab / bolotie
  SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity
  ☆13Updated 2 years ago
• pg-space / panspace
  Embedding-based indexing for compact storage and rapid querying of bacterial pan-genomes
  ☆16Updated 3 weeks ago
• JMencius / LongBow
  Basecalling configuration prediction through FASTQ files
  ☆32Updated this week
• refresh-bio / clusty
  ☆12Updated 6 months ago
• iqbal-lab-org / varifier
  Variant call verification
  ☆16Updated 6 months ago
• karel-brinda / Phylign
  Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
  ☆39Updated last year
• althonos / pyfastani
  Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.
  ☆23Updated last month
• bioinf-mcb / MANIAC
  Computation of average nucleotide identity with the use of MMseqs2
  ☆15Updated 11 months ago
• fpusan / SuperPang
  Non-redundant pangenome assemblies from multiple genomes or bins
  ☆14Updated 6 months ago
• kangxiongbin / StrainXpress
  StrainXpress is a de novo assembly method which base on overlap-layout-consensus (OLC) paradigm and can fast and accurately assemble high…
  ☆13Updated last year
• TravisWheelerLab / BATH
  Better Alignments with Translated HMMER
  ☆23Updated this week
• phiweger / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆15Updated 7 years ago
• dr-joe-wirth / primerForge
  software to identify primers that can distinguish genomes
  ☆20Updated this week
• rcedgar / newick
  Manipulate and generate figures for trees in Newick format
  ☆22Updated 4 months ago
• kangxiongbin / HyLight
  HyLight is a strain aware de novo assembly method based on the overlap-layout-consensus (OLC) paradigm that leverages the strengths of NG…
  ☆12Updated last year
• bluenote-1577 / devider
  Dividing heterogeneous long-read sequencing into groups with de Bruijn graphs
  ☆31Updated 2 months ago
• iqbal-lab-org / make_prg
  Code to create a PRG from a Multiple Sequence Alignment file
  ☆25Updated 2 months ago
• gcgreenberg / LexicHash
  A novel method for sequence similarity estimation
  ☆28Updated last year
• viralInformatics / VIGA
  ☆14Updated 6 months ago
• songlab-cal / swga2
  ☆17Updated 2 years ago
• AllTheBacteria / Phylign
  Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on…
  ☆12Updated last year
• bacpop / mandrake
  Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
  ☆39Updated 8 months ago
• esteinig / sketchy
  Genomic neighbor typing of bacterial pathogens using MinHash
  ☆43Updated 2 years ago
• AfZheng126 / MORA
  MetagenOmic read Re-Assigner and abundance quantifier
  ☆18Updated 10 months ago
• SushiLab / mVIRs
  ☆13Updated last year
• jlumpe / gambit
  A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.
  ☆34Updated 11 months ago
• martinghunt / ziplign
  Simple-to-use interactive comparison of two bacterial genomes
  ☆18Updated this week
• bacpop / unitig-caller
  Methods to determine sequence element (unitig) presence/absence
  ☆22Updated this week