samnooij / PathoFact
Altered version of PathoFact to work more conveniently with SLURM and large input files
☆12Updated 2 months ago
Alternatives and similar repositories for PathoFact:
Users that are interested in PathoFact are comparing it to the libraries listed below
- ☆48Updated 10 months ago
- Contains a fasta format database of a large variety of mobile genetic elements and an annotation file☆43Updated 3 years ago
- A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during…☆63Updated 5 months ago
- Downstream processing of VAMB binning for Viral Elucidation☆47Updated 6 months ago
- code repo for mobileOG-db☆32Updated 6 months ago
- ☆27Updated last year
- Binning Virus Genomes from Metagenomes☆59Updated 2 years ago
- An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.☆42Updated last year
- Reference-quality genome reconstruction from complex metagenomes (or bacterial isolates) using only Nanopore long reads or both long and …☆27Updated last year
- EzAAI - High Throughput Prokaryotic AAI Calculator☆37Updated 3 months ago
- ☆24Updated 4 months ago
- Taxonomic classification of viruses at Order and Family level☆19Updated last year
- Local version of the virus identification and analysis web server (tool set)☆41Updated this week
- Horizontal gene transfer (HGT) identification pipeline☆56Updated last year
- An algorithm for clustering metagenomic sequences.☆33Updated last month
- A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing☆44Updated last month
- Calculation of the Percentage of Conserved Proteins following Qin, Xie et al. 2014 but using DIAMOND instead of BLASTP for alignments.☆23Updated 2 months ago
- Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focu…☆53Updated 3 weeks ago
- MetaGeneMark-2: Improved Gene Prediction in Metagenomes☆18Updated 9 months ago
- PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.☆58Updated last year
- GTDB taxonomy taxdump files with trackable TaxIds☆51Updated 8 months ago
- ☆47Updated 9 months ago
- Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates☆56Updated this week
- ☆42Updated 10 months ago
- PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture☆31Updated 2 years ago
- This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.☆20Updated last year
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆48Updated 9 months ago
- ☆26Updated 9 months ago
- Prediction of prophages from bacterial genomes☆73Updated last year
- A wrapper to identify, bin, classify, and predict host-viral relationship for viruses☆69Updated 3 weeks ago