Alternatives and similar repositories for ReporTree:

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

• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆56Updated 2 weeks ago
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated 2 weeks ago
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 4 years ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆50Updated 8 months ago
• iqbal-lab-org / pling
  Plasmid analysis using rearrangement distances
  ☆33Updated 4 months ago
• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆14Updated last year
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆37Updated last week
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆27Updated last year
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆50Updated 3 months ago
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆28Updated 8 months ago
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆34Updated 3 weeks ago
• josephpetrone / RESCUE
  Resolving Species Level Classification Using Emu
  ☆12Updated 9 months ago
• tseemann / scripts
  Miscellaneous Perl scripts from 20 years in microbial bioinformatics
  ☆17Updated 8 months ago
• bvalot / pyMLST
  whole genome MLST analysis
  ☆41Updated this week
• treangenlab / lemur
  Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets
  ☆24Updated 2 weeks ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆27Updated 3 months ago
• rrwick / Verticall
  Recombination-free trees
  ☆57Updated last year
• mbhall88 / NanoVarBench
  Evaluating Nanopore-based bacterial variant calling
  ☆16Updated 3 months ago
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated last month
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆29Updated last year
• tseemann / phastaf
  Identify phage regions in bacterial genomes for masking purposes
  ☆30Updated 5 years ago
• andrewjpage / krocus
  Predict MLST directly from uncorrected long reads
  ☆27Updated 2 years ago
• mjsull / chromatiblock
  Colinear block visualisation tool
  ☆30Updated last year
• raufs / skDER
  skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.
  ☆44Updated last week
• wanyuac / GeneMates
  An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences
  ☆25Updated 2 years ago
• gtonkinhill / tracs
  Fast pairwise transmission inference from single genome and/or metagenomic data
  ☆19Updated 5 months ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• kwongj / maskrc-svg
  Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG
  ☆20Updated 6 years ago
• gbouras13 / pypolca
  Standalone Python re-implementation of the POLCA polisher from MaSuRCA
  ☆33Updated 6 months ago
• tseemann / sixess
  🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files
  ☆23Updated 6 years ago