piyuranjan / SNIKTLinks
Sequence-independent identification and removal of adapters/systemic contamination in shotgun sequencing data. https://doi.org/10.1093/bioinformatics/btac389
☆18Updated 2 years ago
Alternatives and similar repositories for SNIKT
Users that are interested in SNIKT are comparing it to the libraries listed below
Sorting:
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 7 years ago
- Scaffolding with assembly likelihood optimization☆21Updated 5 years ago
- Code to create a PRG from a Multiple Sequence Alignment file☆25Updated 3 months ago
- ☆30Updated last year
- Scaffolding with Ultralong Reads☆15Updated 5 years ago
- Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.☆35Updated 8 months ago
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆12Updated 2 years ago
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens☆35Updated last month
- Strain-level haplotyping for metagenomes with short or long-reads.☆63Updated 8 months ago
- Colinear block visualisation tool☆31Updated last year
- Quality control plotting for long reads☆10Updated last year
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆13Updated last year
- software to identify primers that can distinguish genomes☆20Updated last week
- Parallel/Homoplasic SNP Finder☆21Updated 2 years ago
- Automated strain separation of low-complexity metagenomes☆53Updated 4 years ago
- Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)☆36Updated 3 weeks ago
- viralFlye pipeline☆18Updated last year
- ☆14Updated 4 years ago
- Microbial agile accurate SNP Typer☆30Updated 2 years ago
- Fast and space-efficient taxonomic classification of long reads☆43Updated 4 months ago
- recompute GFA link overlaps☆25Updated 3 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- This tool is for users to upgrade their metagenomics assemblies using long reads. This includes fixing mis-assemblies and scaffolding/gap…☆13Updated 9 years ago
- Differential k-mer analysis☆39Updated last year
- QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run☆12Updated last year
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆28Updated 5 months ago
- ☆30Updated 2 years ago
- VStrains is a de novo approach for reconstructing strains from viral quasispecies.☆23Updated 10 months ago
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆10Updated 3 months ago
- Predict MLST directly from uncorrected long reads☆27Updated 2 months ago