ALPACA is a caller for genomic variants (single nucleotide and small indels) from next-generation sequencing data that uses a novel algebraic approach to incorporate sample based filtering into the calling. This allows to intuitively control the FDR for arbitrary filtering scenarios.
☆23Nov 19, 2024Updated last year
Alternatives and similar repositories for alpaca
Users that are interested in alpaca are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- SUPBUB is a tool that, in linear time, finds out superbubbles(special graph-structures) in a directed graph.☆12Sep 19, 2019Updated 7 years ago
- BlastGraph is a new tool for computing intensive approximate pattern matching in a sequence graph or a de-Bruijn graph. Given an oriented…☆12May 9, 2013Updated 13 years ago
- LEGACY repository for SODAR Core, preserved for saving review-related issues. See "sodar-core" for the up-to-date repository.☆15Jun 1, 2022Updated 4 years ago
- Streaming relation (overlap, distance, KNN) of (any number of) sorted genomic interval sets. #golang☆46Jun 16, 2026Updated 3 months ago
- nimble aligner that will map your reads to the references on a laptop☆11Jun 29, 2017Updated 9 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organ…☆22Jan 20, 2025Updated last year
- Experimental getopt, gzip reader, FASTA/Q parser and interval queries in nim-lang☆31Apr 20, 2020Updated 6 years ago
- program to estimate admixture coefficients from individual genotype or sequence data☆33Sep 23, 2024Updated 2 years ago
- Tool for analysing viral diversity from High Throughput Sequencing☆12Nov 20, 2025Updated 10 months ago
- A Bayesian method for doing transcriptome assembly from RNA-seq data☆25Feb 2, 2015Updated 11 years ago
- A utility for merging and genotyping Illumina-style GVCFs.☆34Feb 26, 2019Updated 7 years ago
- fast easy interval overlapping for nim-lang☆30Jul 9, 2025Updated last year
- Fast approximation of similarity for sets of very different sizes☆20Mar 8, 2022Updated 4 years ago
- Cosmo is a fast, low-memory DNA assembler using a Succinct (variable order) de Bruijn Graph.☆53Mar 12, 2024Updated 2 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.
- Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.☆24Jan 9, 2021Updated 5 years ago
- Trigger the Google Genomics Pipeline API with CWL☆11Feb 7, 2017Updated 9 years ago
- Standalone C library for assembling Illumina short reads in small regions☆72Dec 15, 2022Updated 3 years ago
- Tool (experimental) to compute layout from overlaps with spectral algorithm☆11Nov 28, 2017Updated 8 years ago
- Pan-genome Seed Index☆20Jul 3, 2026Updated 3 months ago
- Pipeline for Evaluating Prokaryotic References☆11Sep 16, 2016Updated 10 years ago
- collection of data structures and algorithms☆19Mar 19, 2019Updated 7 years ago
- Run-length compressed BWT with LZ77 sampled suffix array☆10Apr 25, 2022Updated 4 years ago
- Improved multi-sample transcript abundance estimates using adaptive priors☆20Oct 29, 2018Updated 7 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 wee tool for random access into BGZF files.☆86May 10, 2018Updated 8 years ago
- python (cython) wrapper for https://github.com/ryanlayer/giggle for fast interval searching of huge datasets.☆16Feb 13, 2018Updated 8 years ago
- SAMsift: advanced filtering and tagging of SAM/BAM alignments using Python expressions.☆23Sep 18, 2025Updated last year
- Mapping-free variant caller for short-read Illumina data☆21Apr 2, 2020Updated 6 years ago
- Quality control on genetic variants from next-generation sequencing data using random forest☆19May 26, 2022Updated 4 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
- Code to do data processing and create figures for "The geography of recent genetic ancestry across Europe", http://arxiv.org/abs/1207.381…☆15May 26, 2014Updated 12 years ago
- nim wrapper for htslib for parsing genomics data files☆159Sep 30, 2026Updated last week
- Iterative error correction of long reads☆13Dec 9, 2022Updated 3 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.
- finding conserved regions in highly diverse genomes☆16May 25, 2026Updated 4 months ago
- Online material and code base for the article Coordinates and Intervals in Graph Based Reference Genomes☆11May 2, 2017Updated 9 years ago
- Very simple and configurable all-in-one dotplot program☆14Apr 1, 2023Updated 3 years ago
- a string to graph aligner☆41Jul 5, 2016Updated 10 years ago
- Parallel MCMC implementation, the core package of the Quantifying Uncertainty project☆15Feb 27, 2017Updated 9 years ago
- Out-of-Core Principal Component Analysis☆19Dec 25, 2017Updated 8 years ago
- Lightweight resources assembly algorithm☆19May 17, 2017Updated 9 years ago