mbhall88 / classification_benchmarkLinks
Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classification
☆12Updated last year
Alternatives and similar repositories for classification_benchmark
Users that are interested in classification_benchmark are comparing it to the libraries listed below
Sorting:
- Genome size estimation from long read overlaps☆62Updated last month
- Strain-level haplotyping for metagenomes with short or long-reads.☆55Updated 6 months ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆22Updated 2 years ago
- A tool to detect acquired AMR genes directly from long read sequencing data.☆17Updated 2 months ago
- software to identify primers that can distinguish genomes☆20Updated 9 months ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆33Updated last month
- ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies☆27Updated last week
- MetagenOmic read Re-Assigner and abundance quantifier☆18Updated 8 months ago
- ☆14Updated 4 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 7 years ago
- Colinear block visualisation tool☆31Updated last year
- Microbial agile accurate SNP Typer☆29Updated last year
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆31Updated 3 months ago
- fast, multithreaded sourmash operations: search, compare, and gather.☆25Updated last week
- StrainXpress is a de novo assembly method which base on overlap-layout-consensus (OLC) paradigm and can fast and accurately assemble high…☆13Updated last year
- Computation of average nucleotide identity with the use of MMseqs2☆15Updated 10 months ago
- The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…☆19Updated last year
- VStrains is a de novo approach for reconstructing strains from viral quasispecies.☆23Updated 8 months ago
- Finding regions of similarity between plasmids☆16Updated 2 years ago
- Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.☆35Updated 6 months ago
- Remove human reads from a sequencing run☆40Updated 2 months ago
- viralFlye pipeline☆18Updated last year
- Fast pairwise transmission inference from single genome and/or metagenomic data☆22Updated 2 months ago
- Genomic neighbor typing of bacterial pathogens using MinHash☆43Updated 2 years ago
- frame-shift correction for long-read (meta)genomics☆33Updated last year
- Resolving Species Level Classification Using Emu☆14Updated last year
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated last year
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- Fast and space-efficient taxonomic classification of long reads☆43Updated 2 months ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆26Updated last year