johanneskoester / alpacaLinks
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.
☆23Updated 8 months ago
Alternatives and similar repositories for alpaca
Users that are interested in alpaca are comparing it to the libraries listed below
Sorting:
- Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.☆47Updated 6 years ago
- reference free variant assembly☆33Updated 2 years ago
- robust matching of small variant datasets using flexible scoring schemes☆11Updated 5 years ago
- ☆37Updated 4 years ago
- Experimental getopt, gzip reader, FASTA/Q parser and interval queries in nim-lang☆32Updated 5 years ago
- pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)☆49Updated 8 years ago
- drunk on perbase pileups and lua expressions☆19Updated 2 months ago
- Online material and code base for the article Coordinates and Intervals in Graph Based Reference Genomes☆11Updated 8 years ago
- a string to graph aligner☆41Updated 9 years ago
- dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organ…☆21Updated 6 months ago
- Malleable All-seeing Journal Of Research Artifacts☆36Updated 2 years ago
- a wee tool for random access into BGZF files.☆85Updated 7 years ago
- Efficient handling of FASTQ files from Python☆51Updated last week
- overlapping bases in read-pairs from a fragment indicate accuracy and reveal error-prone sites☆33Updated 2 months ago
- simple bioinformatics command-line (t)ools (i) (w)ished (i) (h)ad.☆44Updated 2 years ago
- BigWig manpulation tools using libBigWig and htslib☆29Updated last year
- Genome-wide reconstruction of complex structural variants☆39Updated 3 years ago
- Homebrew formulae for bioinformatics software only available for Linux☆27Updated 5 years ago
- Intersect multiple VCF files with haplotype awareness☆25Updated 4 years ago
- Qtip: a tandem simulation approach for accurately predicting read alignment mapping qualities☆25Updated 5 years ago
- sfasta☆35Updated 3 months ago
- Rapid competitive read demulitplexer. Made with tries.☆23Updated 2 months ago
- Build an index for your BAM Index (BAI)☆17Updated 10 years ago
- WDL tools for parsing, type-checking, and more☆25Updated 3 months ago
- prioritize effects of variant annotations from VEP, SnpEff, et al.☆34Updated 8 months ago
- A wrapper to Heng Li's kseq/readfq, an efficient FastQ/Fasta parser☆15Updated 2 years ago
- Variant call adjudication☆16Updated last year
- Stupid Simple Structural Variant View☆25Updated 8 years ago
- ⛰ covtobed | Convert the coverage track from a BAM file into a BED file☆45Updated last month
- SMBL - SnakeMake Bioinformatics Library. Automatic installation of bioinformatics software in your SnakeMake pipelines.☆23Updated 7 years ago