dportik / LRSW-Taxonomic-Profiling-Tutorial
Perform taxonomic profiling analyses for long-read shotgun metagenomic datasets. Developed for the Long Read Sequencing Workshop 2022 at the Jackson Laboratory.
☆13Updated 2 years ago
Related projects ⓘ
Alternatives and complementary repositories for LRSW-Taxonomic-Profiling-Tutorial
- A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing☆39Updated 3 months ago
- ☆17Updated 2 months ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 3 years ago
- Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focu…☆48Updated 3 weeks ago
- Gene Absence Presence Identification tool.☆26Updated last year
- EzAAI - High Throughput Prokaryotic AAI Calculator☆36Updated 3 weeks ago
- Extracts contigs harbouring a target gene / sequence from assemblies and aligns the contigs around the target sequence☆13Updated 6 years ago
- Structural and functional annotation of eukaryotic metagenome-assembled genomes☆21Updated last year
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆48Updated 6 months ago
- Nanomotif - a tool for identifying methylated motifs in metagenomic samples☆23Updated this week
- Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates☆50Updated 6 months ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆24Updated last week
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆24Updated 2 years ago
- Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes☆37Updated 4 months ago
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆29Updated last year
- An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.☆40Updated last year
- Downstream processing of VAMB binning for Viral Elucidation☆46Updated 4 months ago
- Mobile Genetic Elements Retrieving Tool☆15Updated 2 years ago
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆49Updated this week
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆25Updated 2 weeks ago
- ☆45Updated 6 months ago
- SISTR (Salmonella In Silico Typing Resource) command-line tool☆25Updated last month
- IslandPath standalone software☆31Updated last year
- whole genome MLST analysis☆38Updated 5 months ago
- Predict plasmids from uncorrected long read data☆39Updated 4 years ago
- Calculate confidence scores from Kraken2 output☆21Updated 8 months ago
- Small utility script to submit genomes to PHASTER for phage detection☆23Updated 3 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.☆19Updated last year
- Automated strain separation of low-complexity metagenomes☆50Updated 2 years ago