somme89 / rapidNJLinks
Fast implementation of the Neighbour-Joining method for phylogenetic inference
☆17Updated 11 months ago
Alternatives and similar repositories for rapidNJ
Users that are interested in rapidNJ are comparing it to the libraries listed below
Sorting:
- Strain-level haplotyping for metagenomes with short or long-reads.☆53Updated 4 months ago
- Read contamination removal☆25Updated last year
- Variant call verification☆16Updated 3 months ago
- CFSAN Shigella Typing Pipeline☆14Updated 2 years ago
- Remove human reads from a sequencing run☆40Updated last month
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens☆28Updated last week
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆27Updated last month
- transposable element typing pipeline☆19Updated last year
- k-mer based Pipeline to identify the Serotype from Illumina NGS reads☆25Updated 2 years ago
- Genome size estimation from long read overlaps☆59Updated this week
- Resolving Species Level Classification Using Emu☆14Updated last year
- Output FASTQ summary statistics in JSON format☆30Updated 2 years ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆38Updated 5 months ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated last year
- Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.☆35Updated 4 months ago
- Influenza genome analysis Nextflow workflow☆22Updated last month
- SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.☆13Updated 3 years ago
- Code to create a PRG from a Multiple Sequence Alignment file☆25Updated 2 months ago
- Intra-species bacterial contamination detection☆25Updated 6 months ago
- Bacterial Genomics workflow for short(Illumina) and long-read (Oxford Nanopore) sequencing data☆12Updated 2 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 7 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆25Updated 2 years ago
- VStrains is a de novo approach for reconstructing strains from viral quasispecies.☆23Updated 6 months ago
- Minimizer-based assembly scaffolding and mapping using long reads☆43Updated 10 months ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- ☆26Updated 2 years ago
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- ☆31Updated last year
- Trimming tool for Oxford Nanopore sequence data☆21Updated 4 years ago