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:
- software to identify primers that can distinguish genomes☆21Updated 5 months ago
- Finding regions of similarity between plasmids☆16Updated 2 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 7 years ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆30Updated last month
- Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes☆10Updated 4 years ago
- ☆10Updated 2 weeks ago
- MetagenOmic read Re-Assigner and abundance quantifier☆19Updated 4 months ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆23Updated 2 years ago
- ☆16Updated this week
- tool to determine optimal refrerence genome given a set of fasta files☆15Updated 2 years ago
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆12Updated last year
- Visualize microbial evolution at the SNP level!☆14Updated last month
- ☆14Updated 3 years ago
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆27Updated last month
- A tool to detect acquired AMR genes directly from long read sequencing data.☆16Updated last week
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆9Updated 4 years ago
- Genome size estimation from long read overlaps☆57Updated 2 months ago
- fast, multithreaded sourmash operations: search, compare, and gather.☆22Updated this week
- Microbial agile accurate SNP Typer☆29Updated last year
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆25Updated 8 months ago
- ☆20Updated 3 weeks ago
- Genomewide Epistasis Analysis on Bacteria☆14Updated last month
- 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
- Code to create a PRG from a Multiple Sequence Alignment file☆25Updated last week
- The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…☆19Updated last year
- Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on…☆12Updated last year
- CFSAN Shigella Typing Pipeline☆14Updated last year
- Computation of average nucleotide identity with the use of MMseqs2☆13Updated 6 months ago
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆11Updated last year
- Dividing heterogeneous long-read sequencing into groups with de Bruijn graphs☆25Updated 7 months ago