bacpop / PopPIPE
Population analysis PIPEline 🛠🧬
☆18Updated 2 weeks ago
Alternatives and similar repositories for PopPIPE
Users that are interested in PopPIPE are comparing it to the libraries listed below
Sorting:
- Microbial agile accurate SNP Typer☆29Updated last year
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆28Updated last year
- Quality control plotting for long reads☆10Updated 11 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆51Updated last month
- Genomewide Epistasis Analysis on Bacteria☆14Updated this week
- Set of utilities on sequences and BAM files☆27Updated 3 years ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆25Updated 2 years ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆18Updated 2 years ago
- Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.☆34Updated 2 weeks ago
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆34Updated last month
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆30Updated this week
- Phasing for metagenomics using PacBio long reads☆17Updated 3 years ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆27Updated 6 months ago
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆21Updated 2 years ago
- Reproducible scripts and notebooks for 2019 paper on population genetics in metagenomes☆16Updated 5 years ago
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆25Updated 3 weeks ago
- Genome size estimation from long read overlaps☆55Updated 3 weeks ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆35Updated 2 weeks ago
- plasmidVerify: plasmid contig verification tool☆13Updated 5 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆59Updated 2 months ago
- strain-level analysis tools☆36Updated 6 months ago
- Reference-free Binning of Metagenomics Long Reads using Coverage and Composition☆20Updated 8 months ago
- Assembly based core SNP alignments☆7Updated 2 years ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆45Updated 3 weeks ago
- Calculate assocations between genes and traits☆23Updated 2 months ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 6 years ago
- viralFlye pipeline☆18Updated 9 months ago
- Bacterial GWAS analysis☆40Updated 3 weeks ago
- A microbial genomic analysis pipeline used by the Djordjevic Lab☆12Updated 3 months ago
- Clermont PCR method In-Silico☆21Updated last year