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
• RolandFaure / Hairsplitter
  Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.
  ☆35Updated 5 months ago
• HaploConduct / HaploConduct
  Haplotype-aware genome assembly toolkit
  ☆29Updated 5 years ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆55Updated 6 months ago
• at-cg / mm2-plus
  Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)
  ☆35Updated 3 months ago
• uio-cels / NucDiff
  In-depth characterization and annotation of differences between two sets of DNA sequences
  ☆62Updated 5 years ago
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆61Updated 2 weeks ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆50Updated 3 years ago
• iqbal-lab-org / make_prg
  Code to create a PRG from a Multiple Sequence Alignment file
  ☆25Updated last month
• althonos / pyorthoani
  A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.
  ☆30Updated 2 months ago
• broadinstitute / GATK-for-Microbes
  ☆29Updated 4 years ago
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated last month
• pierrepeterlongo / back_to_sequences
  ☆45Updated 2 months ago
• pangenome / PanSN-spec
  Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes
  ☆40Updated 11 months ago
• treangenlab / Olivar
  Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens
  ☆29Updated last month
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆51Updated 4 years ago
• PacificBiosciences / pbipa
  Improved Phased Assembler
  ☆28Updated 3 years ago
• danny-wilson / genomegaMap
  Within-species genome-wide dN/dS estimation from very many genomes
  ☆21Updated 4 years ago
• warp9seq / minimod
  A bioinformatics tool for viewing and calculating base modification frequencies from BAM files
  ☆37Updated 3 weeks ago
• HaploKit / Strainline
  Full-length de novo viral haplotype reconstruction from noisy long reads
  ☆20Updated last year
• cmmr / EsViritu
  Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data
  ☆42Updated this week
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆29Updated last year
• Rinoahu / SwiftOrtho
  A high performance tool to identify orthologs and paralogs across genomes.
  ☆27Updated 2 years ago
• mbhall88 / pistis
  Quality control plotting for long reads
  ☆10Updated last year
• salzberg-lab / PSAURON
  PSAURON is a machine learning model for rapid assessment of protein coding gene annotation
  ☆40Updated 2 weeks ago
• hzi-bifo / Haploflow
  ☆30Updated 2 years ago
• bcgsc / goldrush
  Linear-time de novo Long Read Assembler
  ☆41Updated 8 months 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
• fawaz-dabbaghieh / bubble_gun
  ☆40Updated 2 months ago
• simonwhelan / prequal
  PREQUAL: a pre-alignment quality filter for comparative sequence analyses
  ☆32Updated 3 years ago