Shamir-Lab / SCAPP
SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-021-01068-z
☆31Updated last year
Alternatives and similar repositories for SCAPP:
Users that are interested in SCAPP are comparing it to the libraries listed below
- Downstream processing of VAMB binning for Viral Elucidation☆47Updated 7 months ago
- PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture☆32Updated 3 years ago
- Prophage Activity Estimator☆26Updated 8 months ago
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆48Updated 10 months ago
- Structural and functional annotation of eukaryotic metagenome-assembled genomes☆21Updated last year
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆18Updated last year
- EzAAI - High Throughput Prokaryotic AAI Calculator☆38Updated 4 months ago
- Taxonomic classification of viruses at Order and Family level☆20Updated last year
- ☆19Updated 5 months ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆34Updated 3 weeks ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…☆43Updated last month
- ☆25Updated last year
- MetaGeneMark-2: Improved Gene Prediction in Metagenomes☆18Updated 10 months ago
- Improvement of metagenome-assembled genomes☆51Updated 4 years ago
- IslandPath standalone software☆31Updated last year
- Calculate assocations between genes and traits☆22Updated 3 months ago
- ☆31Updated last year
- Gene Absence Presence Identification tool.☆26Updated last year
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- ☆27Updated this week
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆26Updated last week
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆25Updated 2 years ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆25Updated 3 months ago
- MAG Circularization Method☆33Updated 2 years ago
- ☆24Updated 6 years ago
- Pipeline for metagenome and metatranscriptome joint assembly☆20Updated last year
- This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.☆20Updated last year
- Python script to upload bins and MAGs to ENA (European Nucleotide Archive)☆23Updated 2 weeks ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆22Updated 6 months ago