Alternatives and similar repositories for pango-collapse

Users that are interested in pango-collapse are comparing it to the libraries listed below

• quick-lab / SARS-CoV-2
  SARs-CoV-2 Primer schemes
  ☆15Updated this week
• iqbal-lab-org / viridian
  ☆21Updated 2 months ago
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆38Updated last month
• phac-nml / rebar
  REcombination BARcode detector.
  ☆13Updated last year
• ubinfie / ubinfie.github.io
  µbinfie blog
  ☆17Updated 2 months ago
• karel-brinda / MiniPhy
  Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
  ☆31Updated last month
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆28Updated this week
• cambiotraining / sars-cov-2-genomics
  Course materials for an introduction to SARS-CoV-2 sequencing data analysis
  ☆14Updated 9 months ago
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆56Updated last month
• chrisruis / bammix
  Summarise nucleotide counts at a set of positions in a BAM file to search for mixtures
  ☆13Updated 3 years ago
• RIVM-bioinformatics / AmpliGone
  A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment
  ☆16Updated last week
• martinghunt / tna
  ☆16Updated last month
• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆14Updated last year
• LaborBerlin / score-assemblies
  Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
  ☆26Updated last year
• appliedbinf / el_gato
  ☆10Updated last month
• lskatz / pdtk
  NCBI Pathogen Detection Portal toolkit
  ☆11Updated last year
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆51Updated last month
• corneliusroemer / pango_aliasor
  Utility to alias and dealias pango lineages
  ☆22Updated last year
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated 3 months ago
• nodrogluap / nanostripper
  Strip reads from Oxford Nanopore FAST5 files if they meet certain criteria
  ☆14Updated 3 years ago
• dhelekal / CaveDive
  ☆17Updated 11 months ago
• centre-pathogen-genomics / snippy-ng
  ☆17Updated 3 weeks ago
• mjsull / chromatiblock
  Colinear block visualisation tool
  ☆31Updated last year
• UPHL-BioNGS / Grandeur
  UPHL's Reference Free Pipeline
  ☆26Updated last week
• andrewjpage / krocus
  Predict MLST directly from uncorrected long reads
  ☆27Updated 3 years ago
• dr-joe-wirth / primerForge
  software to identify primers that can distinguish genomes
  ☆21Updated 3 months ago
• mbhall88 / NanoVarBench
  Evaluating Nanopore-based bacterial variant calling
  ☆18Updated last week
• mbhall88 / nohuman
  Remove human reads from a sequencing run
  ☆40Updated 7 months ago
• ktmeaton / ncov-recombinant
  Reproducible workflow for SARS-CoV-2 recombinant sequence detection.
  ☆18Updated 2 years ago
• KoslickiLab / YACHT
  A mathematically characterized hypothesis test for organism presence/absence in a metagenome
  ☆30Updated last week