kangxiongbin / StrainXpress
StrainXpress is a de novo assembly method which base on overlap-layout-consensus (OLC) paradigm and can fast and accurately assemble high complexity metagenome sequencing data at strain resolution.
☆13Updated last year
Alternatives and similar repositories for StrainXpress:
Users that are interested in StrainXpress are comparing it to the libraries listed below
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆23Updated 2 years ago
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆27Updated 2 weeks ago
- ☆16Updated 3 months ago
- ViromeQC is a computational tool to benchmark and quantify non-viral contamination in VLP-enrihed viromes. ViromeQC provides an enrichmen…☆19Updated 2 years ago
- software to identify primers that can distinguish genomes☆21Updated 3 months ago
- MetagenOmic read Re-Assigner and abundance quantifier☆19Updated 3 months ago
- ccfind - circular complete genome finder with clues of terminal redundancy☆15Updated 4 years ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆30Updated 3 weeks ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆44Updated last week
- Strain-level haplotyping for metagenomes with short or long-reads.☆51Updated 3 weeks ago
- Genome size estimation from long read overlaps☆55Updated 3 weeks ago
- Non-redundant pangenome assemblies from multiple genomes or bins☆13Updated 2 months ago
- NCBI-style taxdump files for International Committee on Taxonomy of Viruses (ICTV)☆21Updated 10 months ago
- BinaRena: Interactive Visualization and Binning of Metagenomic Contigs☆32Updated 8 months ago
- ☆16Updated 4 years ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆25Updated 2 years ago
- ☆14Updated last month
- Computation of average nucleotide identity with the use of MMseqs2☆13Updated 4 months ago
- MetaSNV, a metagenomic SNV calling pipeline.☆20Updated 3 years ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆23Updated 9 months ago
- PanTax: Strain-level metagenomic profiling using pangenome graphs☆25Updated 3 weeks ago
- Comparison pipeline for Prokaryote Protein Coding Gene Predictors☆23Updated last year
- Microbial agile accurate SNP Typer☆29Updated last year
- Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.☆22Updated 2 weeks ago
- strain-level analysis tools☆36Updated 6 months ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆28Updated last year
- Genomewide Epistasis Analysis on Bacteria☆14Updated 7 months ago
- MAGScoT - a MAG scoring and refinement tool☆35Updated 6 months ago
- PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.☆18Updated 4 months ago
- A method for reconstruction of subspecies composition and functional profiles from metagenomic data☆13Updated 11 months ago