mbhall88 / ontimeLinks
Extract subsets of ONT (Nanopore) reads based on time
☆22Updated last year
Alternatives and similar repositories for ontime
Users that are interested in ontime are comparing it to the libraries listed below
Sorting:
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆61Updated 3 months ago
- Predict MLST directly from uncorrected long reads☆27Updated 3 years ago
- Genome size estimation from long read overlaps☆61Updated 3 weeks ago
- reference-based long read assemblies of bacterial genomes☆50Updated 4 years ago
- Recombination-free trees☆60Updated 3 weeks ago
- A new high-resolution long-read metagenome assembler for even noisy reads☆94Updated this week
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆39Updated last month
- CFSAN Shigella Typing Pipeline☆15Updated 2 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆30Updated last week
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆27Updated 2 months ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆39Updated 3 months ago
- Calculate confidence scores from Kraken2 output☆22Updated last year
- Automated strain separation of low-complexity metagenomes☆50Updated 3 years ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆52Updated 5 months ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Plasmid analysis using rearrangement distances☆45Updated 2 weeks ago
- Predict plasmids from uncorrected long read data☆40Updated 5 years ago
- Remove human reads from a sequencing run☆40Updated last month
- Colinear block visualisation tool☆31Updated last year
- UPHL's Reference Free Pipeline☆26Updated 2 weeks ago
- Fast and space-efficient taxonomic classification of long reads☆43Updated 3 weeks ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated last year
- Population analysis PIPEline 🛠🧬☆22Updated 4 months ago
- LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations☆27Updated last year
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆35Updated 4 months ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆21Updated last month
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆31Updated 2 weeks ago
- Order and orientation of complete bacterial genomes☆28Updated 2 months ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆26Updated last year