broadinstitute / StrainGE

Related projects ⓘ

Alternatives and complementary repositories for StrainGE

• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆41Updated 4 months ago
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆29Updated 10 months ago
• raufs / skDER
  skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…
  ☆40Updated 3 weeks ago
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆27Updated last year
• LaborBerlin / score-assemblies
  Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
  ☆24Updated 7 months ago
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆25Updated last month
• Shamir-Lab / SCAPP
  SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…
  ☆29Updated last year
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆26Updated 6 months ago
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆25Updated 2 weeks ago
• bacpop / CELEBRIMBOR
  Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs
  ☆22Updated 4 months ago
• brinkmanlab / islandpath
  IslandPath standalone software
  ☆31Updated last year
• kwongj / maskrc-svg
  Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG
  ☆19Updated 5 years ago
• MigleSur / GenAPI
  Gene Absence Presence Identification tool.
  ☆26Updated last year
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆47Updated 3 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆56Updated last year
• mtisza1 / Cenote-Taker3
  Discover and annotate the virome
  ☆31Updated last month
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆45Updated last year
• kevsilva / StrainFLAIR
  Strain-level abundances estimation in metagenomic samples using variation graphs
  ☆25Updated last year
• apcamargo / ictv-mmseqs2-protein-database
  ☆23Updated 9 months ago
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆39Updated this week
• leaemiliepradier / PlasForest
  A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes
  ☆17Updated last year
• pirovc / grimer
  GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…
  ☆21Updated last year
• wanyuac / GeneMates
  An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences
  ☆24Updated 2 years ago
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆19Updated 3 weeks ago
• leylabmpi / SynTracker
  SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…
  ☆25Updated last week
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆32Updated last month
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆25Updated 5 years ago
• lmlui / Jorg
  MAG Circularization Method
  ☆33Updated 2 years ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• qiyunlab / binarena
  BinaRena: Interactive Visualization and Binning of Metagenomic Contigs
  ☆29Updated 3 months ago