iqbal-lab-org / viridian

Related projects ⓘ

Alternatives and complementary repositories for viridian

• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆37Updated this week
• mbhall88 / NanoVarBench
  Evaluating Nanopore-based bacterial variant calling
  ☆15Updated last month
• phac-nml / rebar
  REcombination BARcode detector.
  ☆13Updated 7 months ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆19Updated 4 months ago
• gbouras13 / pypolca
  Standalone Python re-implementation of the POLCA polisher from MaSuRCA
  ☆28Updated 2 months ago
• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆14Updated last year
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆22Updated this week
• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆22Updated last month
• mjsull / chromatiblock
  Colinear block visualisation tool
  ☆30Updated 10 months ago
• KoslickiLab / YACHT
  A mathematically characterized hypothesis test for organism presence/absence in a metagenome
  ☆30Updated this week
• LaborBerlin / score-assemblies
  Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
  ☆24Updated 7 months ago
• USDA-VS / GenoFLU
  Influenza data pipeline to automate genotyping assignment
  ☆22Updated 3 weeks ago
• andrewjpage / krocus
  Predict MLST directly from uncorrected long reads
  ☆25Updated 2 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆56Updated last year
• UPHL-BioNGS / Grandeur
  UPHL's Reference Free Pipeline
  ☆25Updated 2 weeks ago
• gtonkinhill / tracs
  Fast pairwise transmission inference from single genome and/or metagenomic data
  ☆16Updated last month
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆41Updated 4 months ago
• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆24Updated 9 months ago
• tseemann / scripts
  Miscellaneous Perl scripts from 20 years in microbial bioinformatics
  ☆16Updated 4 months ago
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated 3 weeks ago
• farhat-lab / fast-lineage-caller
  ☆13Updated 3 years ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆29Updated last month
• iqbal-lab-org / pling
  Plasmid analysis using rearrangement distances
  ☆30Updated last week
• kwongj / maskrc-svg
  Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG
  ☆19Updated 5 years ago
• ubinfie / ubinfie.github.io
  µbinfie blog
  ☆16Updated 3 weeks ago
• oschwengers / tadrep
  Targeted Detection and Reconstruction of Plasmids
  ☆19Updated 6 months ago
• taxprofiler / taxpasta
  TAXnomic Profile Aggregation and STAndardisation
  ☆34Updated 3 weeks ago
• DOH-JDJ0303 / bigbacter-nf
  ☆19Updated last week
• phiweger / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆15Updated 6 years ago