yinlabniu / HGT-Finder
Program for finding horizontal gene transfer using BLAST result
☆11Updated last year
Related projects ⓘ
Alternatives and complementary repositories for HGT-Finder
- Download NCBI assembly genomes with ftp. rsync, ascp☆11Updated 2 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆19Updated 5 years ago
- Reproducible scripts and notebooks for 2019 paper on population genetics in metagenomes☆15Updated 4 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆28Updated last year
- Quality control plotting for long reads☆10Updated 6 months ago
- Data analysis of Funannotate and Orthofinder outputs to Pangenome results☆17Updated 4 years ago
- ZGA prokaryotic genome assembly and annotation pipeline☆11Updated 2 months ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆24Updated 2 years ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…☆40Updated 3 weeks ago
- genomic alignment similarity search tool☆19Updated 5 months ago
- Pipeline for metagenome and metatranscriptome joint assembly☆18Updated last year
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆25Updated last week
- Dinoflagellate Annotation Workflow☆12Updated 2 years ago
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆23Updated 6 years ago
- transposable element typing pipeline☆16Updated 8 months ago
- Correcting errors in noisy long reads using variation graphs☆51Updated 2 years ago
- DarkHorse2 source code☆9Updated 2 years ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆41Updated 4 months ago
- Genome-Genome circle synteny☆23Updated 11 months ago
- A high performance tool to identify orthologs and paralogs across genomes.☆27Updated last year
- Assembly based core SNP alignments☆7Updated last year
- Set of utilities on sequences and BAM files☆25Updated 3 years ago
- A repository for the lessons and notebooks used for Binder tutorials☆13Updated 4 years ago
- SameStr identifies shared strains between pairs of metagenomic samples based on the similarity of SNV profiles.☆17Updated 2 months ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆17Updated last year
- pGWAS and functional filtering pipeline to identify candidate adaptive genetic traits in bacteria☆11Updated 6 years ago
- Automatic evaluation of HGTs☆25Updated 2 months ago
- MAGScoT - a MAG scoring and refinement tool☆28Updated last month
- Structural and functional annotation of eukaryotic metagenome-assembled genomes☆21Updated last year