cbg-ethz / QuasiRecombView external linksLinks
Probabilistic inference of viral quasispecies subject to recombination (viral haplotype reconstruction).
☆20May 3, 2017Updated 8 years ago
Alternatives and similar repositories for QuasiRecomb
Users that are interested in QuasiRecomb are comparing it to the libraries listed below
Sorting:
- Repo for the software suite ShoRAH (Short Reads Assembly into Haplotypes)☆41Feb 24, 2023Updated 2 years ago
- Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletion…☆26Apr 25, 2018Updated 7 years ago
- Computes a consensus sequence with wobbles, ambiguous bases, and in-frame insertions, from a NGS read alignment.☆18May 14, 2018Updated 7 years ago
- EnsembleAssembler performs de novo assembly of pathogen genomes from metagenomic samples sequenced using Illumina platforms☆10Nov 30, 2014Updated 11 years ago
- variant discovery and annotation using GATK and Ensembl☆17Jun 27, 2013Updated 12 years ago
- Notes on analysing RNAseq, focusing on alternative splicing & polyadenylation.☆12Nov 23, 2021Updated 4 years ago
- A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment☆20Nov 12, 2025Updated 3 months ago
- Wiki form of BLAST documentation from NCBI☆16Feb 21, 2017Updated 8 years ago
- Basestack is a platform for rapid and real time analysis of NGS data. It provides a executable application that connects standard bionfor…☆27Jan 7, 2025Updated last year
- VStrains is a de novo approach for reconstructing strains from viral quasispecies.☆23Feb 5, 2025Updated last year
- Quasitools is a collection of tools for analysing viral quasispecies data.☆27Nov 25, 2021Updated 4 years ago
- ☆24Dec 2, 2022Updated 3 years ago
- convert PAF format to CHAIN format☆34May 14, 2025Updated 9 months ago
- Refinements of the WFA alignment algorithm with better complexity☆26Mar 31, 2022Updated 3 years ago
- Haplotype-aware genome assembly toolkit☆30Jan 8, 2020Updated 6 years ago
- VIRULIGN: fast codon-correct alignment and annotation of viral genomes☆35Apr 2, 2021Updated 4 years ago
- Probabilistic Inference of Molecular Evolution☆10Sep 6, 2021Updated 4 years ago
- mytax is a tool for building custom taxonomies, useful for nucleotide sequence classification☆12Oct 9, 2025Updated 4 months ago
- Interactive visualization of assembly graphs☆83Apr 2, 2022Updated 3 years ago
- Genevieve client: using GenNotes, report ClinVar for individual genomes & add consensus notes☆10Aug 2, 2016Updated 9 years ago
- Code for paper: Localized matrix factorization for recommendation based on matrix block diagonal forms☆10Jan 27, 2015Updated 11 years ago
- Selective Copying Task with Mamba Model. This repository contains a simple implementation for reproducing the selective copying task with…☆12Jun 3, 2024Updated last year
- Speaker materials for 2020 conference☆10Mar 7, 2021Updated 4 years ago
- ngshmmalign is a profile HMM aligner for NGS reads designed particularly for small genomes (such as those of RNA viruses like HIV-1 and H…☆10May 3, 2018Updated 7 years ago
- Analysis tool for Nanopore sequencing data☆11Apr 26, 2024Updated last year
- Bulk and single-cell Multi-Omics ground truth Simulator in R☆10Updated this week
- coding exercise using TCGA immune infiltration data☆11Feb 2, 2024Updated 2 years ago
- ☆12Aug 23, 2023Updated 2 years ago
- This tool designs guides for use with the base editor technology.☆12Aug 11, 2023Updated 2 years ago
- Programming for Biology @ CSHL 2023☆14Oct 17, 2025Updated 3 months ago
- ClusterV: finding HIV quasispecies and drug resistance from ONT sequencing data☆12Jan 7, 2025Updated last year
- SOPanG, a simple tool for pattern matching over an elastic-degenerate string, a recently proposed simplified model for the pan-genome.☆10Apr 16, 2020Updated 5 years ago
- Detects and blacklists paralog RAD loci analyzed in Stacks or ipyrad, based on the McKinney 2017 method (doi:10.1111/1755-0998.12613)☆10Sep 4, 2019Updated 6 years ago
- Parallel Sequence to Graph Alignment☆36Nov 26, 2022Updated 3 years ago
- Cosmo is a fast, low-memory DNA assembler using a Succinct (variable order) de Bruijn Graph.☆53Mar 12, 2024Updated last year
- Micro computer (Raspberry Pi Zero) for distraction free word processing (Vim) and programming (Pico-8).☆11Jan 26, 2017Updated 9 years ago
- Summarise nucleotide counts at a set of positions in a BAM file to search for mixtures☆13Apr 5, 2022Updated 3 years ago
- Probabilistic single-individual haplotyping☆10Mar 15, 2019Updated 6 years ago
- IP-based software loading tool for the Sega Dreamcast☆12Jul 28, 2016Updated 9 years ago