johanneskoester / alpacaView external linksLinks
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
Sorting:
- LEGACY repository for SODAR Core, preserved for saving review-related issues. See "sodar-core" for the up-to-date repository.☆15Jun 1, 2022Updated 3 years ago
- SUPBUB is a tool that, in linear time, finds out superbubbles(special graph-structures) in a directed graph.☆12Sep 19, 2019Updated 6 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 12 years ago
- dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organ…☆21Jan 20, 2025Updated last year
- Streaming relation (overlap, distance, KNN) of (any number of) sorted genomic interval sets. #golang☆47Jul 12, 2020Updated 5 years ago
- Trigger the Google Genomics Pipeline API with CWL☆11Feb 7, 2017Updated 9 years ago
- nimble aligner that will map your reads to the references on a laptop☆11Jun 29, 2017Updated 8 years ago
- Cosmo is a fast, low-memory DNA assembler using a Succinct (variable order) de Bruijn Graph.☆53Mar 12, 2024Updated last year
- python (cython) wrapper for https://github.com/ryanlayer/giggle for fast interval searching of huge datasets.☆15Feb 13, 2018Updated 8 years ago
- program to estimate admixture coefficients from individual genotype or sequence data☆33Sep 23, 2024Updated last year
- a wee tool for random access into BGZF files.☆86May 10, 2018Updated 7 years ago
- create a gemini-compatible database from a VCF☆55Jan 5, 2021Updated 5 years ago
- collection of data structures and algorithms☆19Mar 19, 2019Updated 6 years ago
- A utility for merging and genotyping Illumina-style GVCFs.☆33Feb 26, 2019Updated 6 years ago
- a string to graph aligner☆41Jul 5, 2016Updated 9 years ago
- Mapping-free variant caller for short-read Illumina data☆20Apr 2, 2020Updated 5 years ago
- Standalone C library for assembling Illumina short reads in small regions☆72Dec 15, 2022Updated 3 years ago
- Estimation of per-individual inbreeding coefficients under a probabilistic framework☆22Aug 8, 2023Updated 2 years ago
- Quality control on genetic variants from next-generation sequencing data using random forest☆20May 26, 2022Updated 3 years ago
- Pan-genome Seed Index☆20Mar 12, 2025Updated 11 months ago
- Fast approximation of similarity for sets of very different sizes☆20Mar 8, 2022Updated 3 years ago
- my PhD thesis☆36Jul 10, 2019Updated 6 years ago
- Parallel implementation of the LAST aligner☆18Nov 27, 2016Updated 9 years ago
- Population Reference Graphs for the HLA and MHC.☆35Dec 18, 2018Updated 7 years ago
- ☆36Aug 13, 2020Updated 5 years ago
- Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.☆24Jan 9, 2021Updated 5 years ago
- Proof of concept to use ansible + Lmod to deploy a bioinformatics server☆24Jun 5, 2025Updated 8 months ago
- Improved multi-sample transcript abundance estimates using adaptive priors☆20Oct 29, 2018Updated 7 years ago
- SAMsift: advanced filtering and tagging of SAM/BAM alignments using Python expressions.☆23Sep 18, 2025Updated 4 months 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 11 years ago
- Run-length compressed BWT with LZ77 sampled suffix array☆10Apr 25, 2022Updated 3 years ago
- Genetic coordinates so simple, it feels like MAGIC!☆10Jan 29, 2026Updated 2 weeks ago
- A utility for splitting mixed origin NGS reads☆10Jun 1, 2021Updated 4 years ago
- Pipeline for Evaluating Prokaryotic References☆11Sep 16, 2016Updated 9 years ago
- Assemble the Genome in a Bottle sequencing data☆10Aug 4, 2017Updated 8 years ago
- (a) (p)erfect (c)ircle? ... tests DNA sequences for overlapping ends, then trims and rejoins, and aligns reads to test the join☆11Apr 29, 2021Updated 4 years ago
- Fast Structural Variation Detection Toolbox☆19Feb 16, 2015Updated 11 years ago
- Directly create a bigwig file with signal derived from a sorted and indexed bam file.☆11Jul 7, 2017Updated 8 years ago
- Faster multispecies coalescent inference using multilocus data☆14Aug 13, 2023Updated 2 years ago