program for haplotype phasing from sequence reads and related tools
☆25Nov 29, 2018Updated 7 years ago
Alternatives and similar repositories for hapcut
Users that are interested in hapcut are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Probabilistic single-individual haplotyping☆10Mar 15, 2019Updated 7 years ago
- CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies☆25Apr 13, 2020Updated 6 years ago
- Miscellaneous scripts for applications of PacBio systems☆27Apr 19, 2022Updated 4 years ago
- Pipeline code for creating a fully haplotype-resolved assembly from a combination of PacBio/ONT long reads and Illumina Strand-seq data☆16Apr 2, 2024Updated 2 years ago
- Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution"☆64Oct 15, 2020Updated 5 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- A WGS de novo assembler based on the FMD-index for large genomes☆74Dec 6, 2013Updated 12 years ago
- ☆35Feb 20, 2020Updated 6 years ago
- FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds☆72Nov 12, 2020Updated 5 years ago
- Hidden Markov Model based Copy number caller☆20Dec 9, 2025Updated 4 months ago
- Coronavirus (SARS-Cov-2) sequencing analysis☆10Oct 5, 2021Updated 4 years ago
- Obsolete/Legacy GATK repository -- go to https://github.com/broadinstitute/gatk instead☆32Aug 16, 2017Updated 8 years ago
- Convert structural variants to sequence graphs [ VCF + FASTA ---> GFA ]☆11Mar 6, 2024Updated 2 years ago
- HiFi error modeler and simulator with ploidy☆11Feb 12, 2026Updated 2 months ago
- Identifying repeats in high-throughput sequencing data☆16Apr 12, 2024Updated 2 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Implementation of a polymorphism aware phylogenetic model using HYPHY☆19Jan 14, 2022Updated 4 years ago
- Adaptive haplotype assembly for efficiently leveraging high coverage in long reads☆13Sep 4, 2018Updated 7 years ago
- Segmental Duplication Assembler (SDA).☆43May 7, 2023Updated 2 years ago
- phasing and Allele Specific Expression from RNA-seq☆120Mar 21, 2026Updated last month
- software tools for haplotype assembly from sequence data☆231Feb 9, 2025Updated last year
- EXPERIMENTAL implementation of side graph☆10Apr 16, 2015Updated 11 years ago
- Fast, accurate and simple to use command line tool for variant detection in NGS data.☆12Sep 3, 2019Updated 6 years ago
- Flexible genotype query among 30,000+ samples whole-genome☆94Sep 4, 2019Updated 6 years ago
- MEM mapper prototype☆13Nov 28, 2020Updated 5 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- ☆11Sep 7, 2023Updated 2 years ago
- Utilities to detect and profile `het-kmers`☆12Aug 5, 2024Updated last year
- Naive PCA for genotype data☆10Jul 27, 2016Updated 9 years ago
- Long read to reference genome mapping tool☆13Mar 14, 2024Updated 2 years ago
- Pipeline to phase a genome into two homeologous subgenomes. Parental genomes are required.☆10May 22, 2025Updated 11 months ago
- DNA assembler developed on FER (Croatia), RBI (Croatia) and GIS (Singapore)☆18Jan 18, 2016Updated 10 years ago
- A wrapper for calling small variants from human germline high-coverage single-sample Illumina data☆14Jul 21, 2019Updated 6 years ago
- Exact Tandem Repeat Finder (not a TRF replacement)☆51Oct 22, 2019Updated 6 years ago
- Falcon2Fastg is a tool for converting a FALCON assembly to FASTG format to visualize with Bandage☆13May 16, 2016Updated 9 years ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- a string to graph aligner☆41Jul 5, 2016Updated 9 years ago
- Improved Phased Assembler☆28Mar 11, 2022Updated 4 years ago
- A framework to annotate SVs with previous known SVs (vcf file) and or with genomic features (gff and or bed files)☆13Mar 12, 2018Updated 8 years ago
- The CHM1-NA12878 benchmark for single-sample SNP/INDEL calling from WGS Illumina data☆32Feb 20, 2018Updated 8 years ago
- Expectation-Maximization algorithm for Allele-Specific Expression☆22May 9, 2023Updated 2 years ago
- A comprehensive and intelligent clinical phasing tool☆14Dec 3, 2022Updated 3 years ago
- a toolset for efficient analysis of 10X Genomics linked read data sets, in particular for de novo assembly☆15Nov 27, 2019Updated 6 years ago