Sequence Distance Graph framework: graph + reads + mapping + analysis
☆25Jun 4, 2022Updated 3 years ago
Alternatives and similar repositories for sdg
Users that are interested in sdg are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- This repo is deprecated. Please use gfatools instead.☆15Aug 17, 2018Updated 7 years ago
- ☆24Apr 2, 2021Updated 5 years ago
- semi-reference-based short read compression☆11Mar 5, 2019Updated 7 years ago
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Aug 4, 2021Updated 4 years ago
- URMAP ultra-fast read mapper☆38Jun 15, 2020Updated 5 years ago
- 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.
- SIMD-parallel BLAST X-drop DP on sequence graphs☆24May 30, 2024Updated last year
- recompute GFA link overlaps☆25Sep 14, 2022Updated 3 years ago
- Identifying large scale inversions between two genomes by mapping genome 1's unique kmers onto genome 2.☆10Jun 6, 2025Updated 11 months ago
- The Dagstuhl Format for Assembly☆13Oct 16, 2017Updated 8 years ago
- An efficient index for the colored, compacted, de Bruijn graph☆112Mar 11, 2026Updated last month
- Layout module for raw de novo genome assembly of long uncorrected reads.☆21Feb 2, 2021Updated 5 years ago
- extract MSAs from genome variation graphs☆34Mar 24, 2026Updated last month
- Orpheum (Previously called and published under sencha) is a Python package for directly translating RNA-seq reads into coding protein seq…☆19Oct 4, 2022Updated 3 years ago
- de Bruijn graph cOrrectiOn from graph aLignment☆11Jul 20, 2020Updated 5 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.
- A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)☆144Aug 24, 2025Updated 8 months ago
- GFA insert into GenomicSQLite☆49Jun 7, 2021Updated 4 years ago
- Histosketching Using Little Kmers☆57May 25, 2023Updated 2 years ago
- A database for signatures of public genomic sources☆18Jan 1, 2026Updated 4 months ago
- Parallel Sequence to Graph Alignment☆36Nov 26, 2022Updated 3 years ago
- Naive PCA for genotype data☆10Jul 27, 2016Updated 9 years ago
- De novo estimates of genetic relatedness from next-gen sequencing data☆45Jul 28, 2019Updated 6 years ago
- Graph-based mapping of long sequences, noisy or HiFi.☆55Oct 5, 2020Updated 5 years ago
- CPANG19 - Computational PANGenomics (2019)☆12May 7, 2020Updated 6 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- alignment to variation graph inducer☆159Apr 11, 2026Updated 3 weeks ago
- ☆13Jan 23, 2020Updated 6 years ago
- De novo genome assembler.☆12Jul 30, 2018Updated 7 years ago
- An accurate aligner of long reads to a variation graph, based on co-linear chaining☆35May 23, 2025Updated 11 months ago
- Phase reads, assemble haplotypes and detect SVs☆19Nov 11, 2020Updated 5 years ago
- A C++ library and utilities for manipulating the Graphical Fragment Assembly format.☆55May 17, 2022Updated 3 years ago
- Ruby library for handling GFA files☆17Jul 10, 2025Updated 9 months ago
- Scaffolding of genomic assemblies with RNA seq data☆15Oct 8, 2015Updated 10 years ago
- Graphical interactive tool for the visualization of sequence graphs in GFA format.☆74Feb 19, 2019Updated 7 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.☆24Jan 9, 2021Updated 5 years ago
- A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.☆53Apr 27, 2026Updated last week
- Somatic (mosaic) SNV caller for 10X Genomics data using random forest classification and feature-based filters☆23Apr 1, 2019Updated 7 years ago
- ♥ Efficient Estimation of Evolutionary Distances☆47Feb 15, 2026Updated 2 months ago
- Accurate and fast taxonomic classification using pseudoaligning☆21Sep 16, 2017Updated 8 years ago
- Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.☆29Mar 5, 2018Updated 8 years ago
- Indel-aware consensus for aligned BAM☆21Aug 16, 2025Updated 8 months ago