gbouras13 / pypolcaLinks
Standalone Python re-implementation of the POLCA polisher from MaSuRCA
☆41Updated 4 months ago
Alternatives and similar repositories for pypolca
Users that are interested in pypolca are comparing it to the libraries listed below
Sorting:
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆53Updated 4 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆64Updated 6 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆63Updated 8 months ago
- Automated strain separation of low-complexity metagenomes☆52Updated 4 years ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated 2 years ago
- Genome size estimation from long read overlaps☆79Updated last month
- Recombination-free trees☆63Updated 4 months ago
- Microbial agile accurate SNP Typer☆30Updated 2 years ago
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆31Updated 5 months ago
- Colinear block visualisation tool☆31Updated last year
- Fast and space-efficient taxonomic classification of long reads☆42Updated 4 months ago
- Plasmid analysis using rearrangement distances☆49Updated 4 months ago
- A new high-resolution long-read metagenome assembler for even noisy reads☆116Updated 2 weeks ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆28Updated 5 months ago
- A pipeline for bioinformatics analysis of bacterial genomes☆32Updated last week
- Remove human reads from a sequencing run☆47Updated 3 weeks ago
- Bacterial GWAS analysis☆46Updated 2 months ago
- Genomewide Epistasis Analysis on Bacteria☆15Updated 7 months ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- Gene-flank analysis tool☆34Updated last year
- A taxonomic classifier of plasmids☆28Updated 4 years ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆27Updated 3 years ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆35Updated 8 months ago
- reference-based long read assemblies of bacterial genomes☆51Updated 4 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- Extract subsets of ONT (Nanopore) reads based on time☆23Updated last year
- Intra-species bacterial contamination detection☆25Updated 10 months ago
- Calculate confidence scores from Kraken2 output☆23Updated last year
- Fast pairwise transmission inference from single genome and/or metagenomic data☆22Updated 5 months ago
- 🦠🧬🧑💻📇 Microbial genomes-to-report pipeline☆73Updated last month