lskatz / lskScriptsLinks
A placeholder for all my random scripts. Some scripts might eventually graduate and go to their own projects, so don't be surprised if anything leaves in the future.
☆17Updated last month
Alternatives and similar repositories for lskScripts
Users that are interested in lskScripts are comparing it to the libraries listed below
Sorting:
- A tool for removing redundant genomes from a set of assemblies☆76Updated 2 years ago
- Fast k-mer based tool for multi locus sequence typing (MLST)☆45Updated 5 years ago
- Split Kmer Analysis☆65Updated 3 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing☆49Updated 2 months ago
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆50Updated last year
- Phigaro is a scalable command-line tool for predicting phages and prophages☆52Updated last year
- PANgenome with Annotations, COre identification, Tree and corresponding Alignments☆74Updated last year
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆38Updated 2 months ago
- a collection of scripts for organising bacterial genomes by species☆77Updated 3 years ago
- Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates☆73Updated 2 months ago
- Estimate metagenomic coverage and sequence diversity☆54Updated last year
- SeqSero2☆38Updated last year
- Code Safety Inspection Service☆20Updated 2 years ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated last year
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆57Updated 3 weeks ago
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆34Updated 2 years ago
- Identify phage regions in bacterial genomes for masking purposes☆34Updated 5 years ago
- Mapping-Assisted Targeted-Assembly for Metagenomics☆23Updated 5 months ago
- ☆32Updated 6 months ago
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes☆52Updated last month
- Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data☆36Updated last week
- ☆35Updated last year
- Prophage Activity Estimator☆26Updated last year
- PLSDB pipeline to collect bacterial plasmids from NCBI☆38Updated 10 months ago
- Taxonomic classification of viruses at Order and Family level☆20Updated 2 years ago
- SC2 variant detection and composition pipeline☆17Updated 2 years ago
- Recombination-free trees☆59Updated 5 months ago
- reference-based long read assemblies of bacterial genomes☆50Updated 4 years ago