Alternatives and similar repositories for pango-collapse

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

• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆40Updated 3 months ago
• iqbal-lab-org / viridian
  ☆23Updated 9 months ago
• CDCgov / seqsender
  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
  ☆38Updated 3 weeks ago
• nebiolabs / ampseer
  Ampseer examines reads in fastq format and identifies which multiplex PCR primer set was used to generate the SARS-CoV-2 sequencing libra…
  ☆15Updated last year
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆32Updated last week
• karel-brinda / MiniPhy
  Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
  ☆43Updated 8 months ago
• quick-lab / SARS-CoV-2
  SARs-CoV-2 Primer schemes
  ☆16Updated 7 months ago
• esteinig / sketchy
  Genomic neighbor typing of bacterial pathogens using MinHash
  ☆43Updated 2 years ago
• enasequence / ena-bulk-webincli
  Validate and submit reads using Webin-CLI in batch.
  ☆11Updated 2 years ago
• KoslickiLab / YACHT
  A mathematically characterized hypothesis test for organism presence/absence in a metagenome
  ☆34Updated last week
• mbhall88 / nohuman
  Remove human reads from a sequencing run
  ☆46Updated 2 weeks ago
• rrwick / Verticall
  Recombination-free trees
  ☆64Updated 3 months ago
• RIVM-bioinformatics / AmpliGone
  A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment
  ☆20Updated last month
• karel-brinda / Phylign
  Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
  ☆39Updated last year
• phac-nml / rebar
  REcombination BARcode detector.
  ☆16Updated last year
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆63Updated 8 months ago
• martinghunt / ziplign
  Simple-to-use interactive comparison of two bacterial genomes
  ☆18Updated last week
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆79Updated 3 weeks ago
• cambiotraining / sars-cov-2-genomics
  Course materials for an introduction to SARS-CoV-2 sequencing data analysis
  ☆14Updated last year
• dhelekal / CaveDive
  ☆18Updated last year
• corneliusroemer / pango_aliasor
  Utility to alias and dealias pango lineages
  ☆23Updated 2 years ago
• nodrogluap / nanostripper
  Strip reads from Oxford Nanopore FAST5 files if they meet certain criteria
  ☆14Updated 4 years ago
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated 10 months ago
• centre-pathogen-genomics / snippy-ng
  ☆24Updated last week
• gbouras13 / baktfold
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids using protein structural information
  ☆33Updated this week
• ubinfie / ubinfie.github.io
  µbinfie blog
  ☆18Updated 5 months ago
• mjsull / chromatiblock
  Colinear block visualisation tool
  ☆31Updated last year
• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆28Updated 5 months ago
• LaborBerlin / score-assemblies
  Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
  ☆26Updated last year
• jlumpe / gambit
  A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.
  ☆35Updated last year