danisven / StringMeUpLinks
A post-processing tool to reclassify Kraken 2 output based on the confidence score and/or minimum minimizer hit groups.
☆9Updated 4 years ago
Alternatives and similar repositories for StringMeUp
Users that are interested in StringMeUp are comparing it to the libraries listed below
Sorting:
- Calculate confidence scores from Kraken2 output☆22Updated last year
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆59Updated last month
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆36Updated 3 months ago
- Predict MLST directly from uncorrected long reads☆27Updated 3 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆30Updated this week
- Generation of pan-genome profile files using Roary output.☆9Updated 7 years ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆52Updated 3 months ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆24Updated 7 years ago
- INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search☆15Updated 2 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Colinear block visualisation tool☆31Updated last year
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 4 years ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆36Updated 2 months ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆46Updated 2 years ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆38Updated last month
- Bacterial GWAS analysis☆42Updated last week
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆26Updated 2 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆28Updated 2 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- Phylogeny Enhanded Prediction of PAN-genome☆41Updated 5 years ago
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆9Updated 4 years ago
- SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.☆13Updated 3 years ago
- Intra-species bacterial contamination detection☆25Updated 5 months ago
- Calculate assocations between genes and traits☆23Updated 4 months ago
- reference-based long read assemblies of bacterial genomes☆50Updated 3 years ago
- Recombination-free trees☆58Updated 3 months ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆46Updated last week
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.