Alternatives and similar repositories for StrainGE:

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

• bacpop / CELEBRIMBOR
  Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs
  ☆23Updated 9 months ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆51Updated 3 weeks ago
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆35Updated last week
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆28Updated last year
• raufs / skDER
  skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.
  ☆44Updated last week
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆59Updated 2 months ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆27Updated 4 months ago
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆26Updated 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
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆40Updated 2 weeks ago
• kevsilva / StrainFLAIR
  Strain-level abundances estimation in metagenomic samples using variation graphs
  ☆25Updated 2 years ago
• tseemann / sixess
  🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files
  ☆24Updated 7 years ago
• leylabmpi / SynTracker
  SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…
  ☆29Updated 3 months ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆28Updated this week
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆29Updated 10 months ago
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆27Updated 6 months ago
• rrwick / Verticall
  Recombination-free trees
  ☆58Updated last month
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆55Updated 3 weeks ago
• santeripuranen / SpydrPick
  SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.
  ☆13Updated 3 years ago
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆49Updated 2 years ago
• mbhall88 / nohuman
  Remove human reads from a sequencing run
  ☆40Updated 7 months ago
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆23Updated last month
• pirovc / grimer
  GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…
  ☆23Updated 2 years ago
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆29Updated last year
• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆24Updated 7 months ago
• MigleSur / GenAPI
  Gene Absence Presence Identification tool.
  ☆26Updated last month
• tseemann / seeka
  Get microbial sequence data easier and faster
  ☆28Updated 5 years ago
• leaemiliepradier / PlasForest
  A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes
  ☆18Updated 2 years ago
• ikmb / MAGScoT
  MAGScoT - a MAG scoring and refinement tool
  ☆35Updated 6 months ago