Alternatives and similar repositories for NanoVarBench:

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

• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆47Updated last month
• mjsull / chromatiblock
  Colinear block visualisation tool
  ☆30Updated last year
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆41Updated last month
• rrwick / Verticall
  Recombination-free trees
  ☆56Updated last year
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆48Updated 6 months ago
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆34Updated last month
• gbouras13 / pypolca
  Standalone Python re-implementation of the POLCA polisher from MaSuRCA
  ☆29Updated 4 months ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆30Updated last month
• KoslickiLab / YACHT
  A mathematically characterized hypothesis test for organism presence/absence in a metagenome
  ☆30Updated last month
• iqbal-lab-org / pling
  Plasmid analysis using rearrangement distances
  ☆31Updated 2 months ago
• fmenardo / Treemmer
  Python tool to reduce size and redundancy of phylogenetic datasets
  ☆29Updated last year
• tseemann / scripts
  Miscellaneous Perl scripts from 20 years in microbial bioinformatics
  ☆17Updated 6 months ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆25Updated 2 months ago
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆29Updated last year
• raufs / skDER
  skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…
  ☆41Updated 3 weeks ago
• NickJD / ORForise
  Comparison pipeline for Prokaryote Protein Coding Gene Predictors
  ☆22Updated 8 months ago
• brinkmanlab / islandpath
  IslandPath standalone software
  ☆31Updated last year
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated 2 months ago
• gtonkinhill / tracs
  Fast pairwise transmission inference from single genome and/or metagenomic data
  ☆19Updated 3 months ago
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆47Updated 3 years ago
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆24Updated last month
• HaploKit / Strainline
  Full-length de novo viral haplotype reconstruction from noisy long reads
  ☆17Updated last year
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆20Updated 2 months ago
• andrewjpage / krocus
  Predict MLST directly from uncorrected long reads
  ☆26Updated 2 years ago
• phiweger / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆15Updated 6 years ago
• HaploKit / vechat
  Correcting errors in noisy long reads using variation graphs
  ☆51Updated 2 years ago
• jonas-fuchs / varVAMP
  Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.
  ☆34Updated 4 months ago
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆27Updated last year
• MicrobialDarkMatter / nanomotif
  Nanomotif - a tool for identifying methylated motifs in metagenomic samples
  ☆24Updated this week