Alternatives and similar repositories for PopPIPE:

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

• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated last week
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆29Updated last year
• ablab / plasmidVerify
  plasmidVerify: plasmid contig verification tool
  ☆12Updated 4 years ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆32Updated 2 months ago
• KoslickiLab / YACHT
  A mathematically characterized hypothesis test for organism presence/absence in a metagenome
  ☆30Updated 3 weeks ago
• taxprofiler / taxpasta
  TAXnomic Profile Aggregation and STAndardisation
  ☆35Updated 3 months ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆50Updated 7 months ago
• yosuken / ccfind
  ccfind - circular complete genome finder with clues of terminal redundancy
  ☆15Updated 4 years ago
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆27Updated last year
• phiweger / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆15Updated 6 years ago
• kwongj / maskrc-svg
  Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG
  ☆20Updated 6 years ago
• mjsull / chromatiblock
  Colinear block visualisation tool
  ☆30Updated last year
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆48Updated 2 months ago
• mbhall88 / pistis
  Quality control plotting for long reads
  ☆10Updated 9 months ago
• pirovc / grimer
  GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…
  ☆22Updated 2 years ago
• maxgmarin / panqc
  A toolkit for quality control & adjustment of nucleotide redundancy in bacterial pan-genome analyses
  ☆16Updated 10 months ago
• leaemiliepradier / PlasForest
  A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes
  ☆18Updated last year
• francesccoll / powerbacgwas
  PowerBacGWAS: Power calculations for Bacterial GWAS
  ☆13Updated 3 years ago
• anuradhawick / MetaBCC-LR
  Reference-free Binning of Metagenomics Long Reads using Coverage and Composition
  ☆20Updated 5 months ago
• katholt / reddog-nf
  pipeline for read mapping, snp calling and annotation for bacterial genomes
  ☆12Updated 11 months ago
• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆14Updated last year
• RolandFaure / Hairsplitter
  Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.
  ☆34Updated 2 months ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆19Updated 7 months ago
• Sudaraka88 / LDWeaver
  Genomewide Epistasis Analysis on Bacteria
  ☆14Updated 5 months ago
• gtonkinhill / tracs
  Fast pairwise transmission inference from single genome and/or metagenomic data
  ☆19Updated 4 months ago
• piyuranjan / SNIKT
  Sequence-independent identification and removal of adapters/systemic contamination in shotgun sequencing data. https://doi.org/10.1093/bi…
  ☆16Updated last year
• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆24Updated 4 months ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆40Updated 4 years ago
• ChrispinChaguza / RCandy
  RCandy: an R package for visualising homologous recombination events in bacterial genomes
  ☆19Updated 2 years ago