kwongj / contig-puller
Extracts contigs harbouring a target gene / sequence from assemblies and aligns the contigs around the target sequence
☆13Updated 6 years ago
Alternatives and similar repositories for contig-puller:
Users that are interested in contig-puller are comparing it to the libraries listed below
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆48Updated 10 months ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆25Updated 2 years ago
- pGWAS and functional filtering pipeline to identify candidate adaptive genetic traits in bacteria☆11Updated 7 years ago
- ☆19Updated 5 months ago
- whole genome MLST analysis☆40Updated 9 months ago
- EzAAI - High Throughput Prokaryotic AAI Calculator☆38Updated 4 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆56Updated last month
- Perform taxonomic profiling analyses for long-read shotgun metagenomic datasets. Developed for the Long Read Sequencing Workshop 2022 at …☆13Updated 2 years ago
- Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates☆60Updated last month
- PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture☆32Updated 3 years ago
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆31Updated last year
- Gene Absence Presence Identification tool.☆26Updated last year
- IslandPath standalone software☆31Updated last year
- Structural and functional annotation of eukaryotic metagenome-assembled genomes☆21Updated last year
- Discover and annotate the virome☆36Updated 4 months ago
- Identify phage regions in bacterial genomes for masking purposes☆30Updated 5 years ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆34Updated 3 weeks ago
- post processing of bacterial pangenome gene presence/absence matrices☆55Updated 5 months ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆18Updated last year
- Mobile Genetic Elements Retrieving Tool☆15Updated 3 years ago
- This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.☆20Updated last year
- Predict plasmids from uncorrected long read data☆39Updated 5 years ago
- Downstream processing of VAMB binning for Viral Elucidation☆48Updated 7 months ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 6 years ago
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- ☆36Updated 2 years ago
- Phylotype your strains using Clermont's 2013 method: ezclermont.org☆10Updated 2 years ago
- A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing☆44Updated 3 weeks ago
- Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes☆42Updated last week