SALSA: A tool to scaffold long read assemblies with Hi-C data
☆189May 17, 2024Updated 2 years ago
Alternatives and similar repositories for SALSA
Users that are interested in SALSA are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- k-mer based assembly evaluation☆344May 21, 2026Updated last month
- Mapping pipeline for data generated using Arima-HiC☆84May 22, 2024Updated 2 years ago
- haplotypic duplication identification tool☆289Oct 30, 2025Updated 8 months ago
- 3D de novo assembly (3D DNA) pipeline☆225Nov 29, 2023Updated 2 years ago
- Find, circularise and annotate mitogenome from PacBio assemblies☆197May 11, 2025Updated last year
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)☆80Oct 12, 2018Updated 7 years ago
- ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data☆179Oct 20, 2024Updated last year
- Yet another Hi-C scaffolding tool☆181Nov 4, 2024Updated last year
- Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and O…☆398Apr 22, 2026Updated 2 months 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
- Tools for fast and flexible genome assembly scaffolding and improvement☆567Feb 14, 2024Updated 2 years ago
- Fast genome analysis from unassembled short reads☆323Apr 8, 2024Updated 2 years ago
- Peregrine: Fast Genome Assembler Using SHIMMER Index☆102Feb 6, 2022Updated 4 years ago
- base-accurate DNA sequence alignments using WFA and mashmap3☆217Jun 21, 2026Updated last week
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.☆211Nov 18, 2022Updated 3 years ago
- software tools for haplotype assembly from sequence data☆232Feb 9, 2025Updated last year
- Unzip assembly graphs with Hi-C data and/or long reads.☆28May 7, 2026Updated last month
- Synteny and Rearrangement Identifier☆474Jun 20, 2026Updated last week
- ☆78Dec 4, 2019Updated 6 years ago
- VGP repository for the genome assembly working group☆193Mar 31, 2026Updated 2 months ago
- Chromosome-level scaffolding using multiple references☆169Sep 8, 2024Updated last year
- Fast and accurate de novo assembler for long reads☆403May 10, 2024Updated 2 years ago
- A gap-closing software tool that uses long reads to enhance genome assembly.☆240Sep 6, 2024Updated last year
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- ⛓ Correct misassemblies using linked AND long reads☆64Mar 24, 2026Updated 3 months ago
- A Hi-C scaffolding method☆22Dec 22, 2021Updated 4 years ago
- assembly evaluation tool☆35May 11, 2022Updated 4 years ago
- Yet another k-mer analyzer☆173Dec 30, 2025Updated 5 months ago
- test repository☆29Jul 6, 2023Updated 2 years ago
- [MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads☆273Oct 13, 2022Updated 3 years ago
- Inference of ploidy and heterozygosity structure using whole genome sequencing data☆296May 28, 2026Updated last month
- Fast and accurately polish the genome generated by long reads.☆244Jan 9, 2025Updated last year
- An accurate GFF3/GTF lift over pipeline☆546Aug 1, 2023Updated 2 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 EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment☆87Apr 8, 2021Updated 5 years ago
- ☆46Jun 21, 2020Updated 6 years ago
- Evaluate variant calls and its combination with k-mer multiplicity☆69Dec 2, 2022Updated 3 years ago
- HiC-Hiker: A probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C☆26Jan 14, 2021Updated 5 years ago
- Genome mapping and spliced alignment of cDNA or amino acid sequences☆113Feb 28, 2026Updated 4 months ago
- A single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulatio…☆125Jun 18, 2026Updated last week
- Workflows for correcting and scaffolding long-read (PacBio, nanopore) genome assemblies using optical mapping and/or Dovetail Hi-C data☆20Aug 18, 2020Updated 5 years ago