Alternatives and similar repositories for VStrains

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

• HaploKit / vechat
  Correcting errors in noisy long reads using variation graphs
  ☆51Updated 2 years ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆52Updated 5 months ago
• RolandFaure / Hairsplitter
  Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.
  ☆35Updated 4 months ago
• HaploConduct / HaploConduct
  Haplotype-aware genome assembly toolkit
  ☆29Updated 5 years ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆50Updated 3 years ago
• althonos / pyorthoani
  A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.
  ☆30Updated last month
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆61Updated 2 weeks ago
• iqbal-lab-org / make_prg
  Code to create a PRG from a Multiple Sequence Alignment file
  ☆25Updated last week
• broadinstitute / GATK-for-Microbes
  ☆29Updated 3 years ago
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆29Updated last year
• 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
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆42Updated 4 years ago
• at-cg / mm2-plus
  Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)
  ☆34Updated 2 months ago
• aesheppard / TETyper
  transposable element typing pipeline
  ☆19Updated last year
• mbhall88 / pistis
  Quality control plotting for long reads
  ☆10Updated last year
• uio-cels / NucDiff
  In-depth characterization and annotation of differences between two sets of DNA sequences
  ☆62Updated 5 years ago
• Dmitry-Antipov / viralFlye
  viralFlye pipeline
  ☆18Updated last year
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆29Updated 2 years ago
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated 3 weeks ago
• HKU-BAL / MegaPath-Nano
  MegaPath-Nano: Accurate Compositional Analysis and Drug-level Antimicrobial Resistance Detection Software for Oxford Nanopore Long-read M…
  ☆14Updated 3 years ago
• pangenome / PanSN-spec
  Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes
  ☆39Updated 11 months ago
• HaploKit / Strainline
  Full-length de novo viral haplotype reconstruction from noisy long reads
  ☆20Updated last year
• farhat-lab / fast-lineage-caller
  ☆14Updated 4 years ago
• PacificBiosciences / pbipa
  Improved Phased Assembler
  ☆28Updated 3 years ago
• bacpop / PopPIPE
  Population analysis PIPEline 🛠🧬
  ☆22Updated 4 months ago
• mbhall88 / classification_benchmark
  Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classification
  ☆12Updated last year
• salzberg-lab / PSAURON
  PSAURON is a machine learning model for rapid assessment of protein coding gene annotation
  ☆39Updated 5 months ago
• karel-brinda / Phylign
  Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
  ☆37Updated last year
• LANL-Bioinformatics / PhaME
  Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to constr…
  ☆33Updated last year
• niemasd / ViralConsensus
  Fast viral consensus genome reconstruction
  ☆23Updated 2 months ago