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Search results for variants variant calling

variant-calling x

6 search results found

✂️ ⚡ Rapid haploid variant calling and core genome alignment

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Octopus ⭐ 285

Bayesian haplotype-based mutation calling

PEPPER-Margin-DeepVariant

Megalodon ⭐ 172

Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.

A tool set for short variant discovery in genetic sequence data.

Clairvoyante ⭐ 142

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

Fermikit ⭐ 91

De novo assembly based variant calling pipeline for Illumina short reads

Genomicsdb ⭐ 88

High performance data storage for importing, querying and transforming variants.

Mccortex ⭐ 86

De novo genome assembly and multisample variant calling

Tiledb Vcf ⭐ 79

Efficient variant-call data storage and retrieval library using the TileDB storage library.

Callings Nf ⭐ 76

GATK RNA-Seq Variant Calling in Nextflow

Toolkit for calling structural variants using short or long reads

Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling

xHLA: Fast and accurate HLA typing from short read sequence data

Bayestyper ⭐ 52

A method for variant graph genotyping based on exact alignment of k-mers

Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.

Chm Eval ⭐ 37

Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products

A tool for fast and accurate summarizing of variant calling format (VCF) files

Use an ensemble of variant callers to call variants from ATAC-seq data

Clairs To ⭐ 18

ClairS-TO - a deep-learning method for tumor-only somatic SNV calling

Assembly and intrahost / low-frequency variant calling for viral samples

Please consider using/contributing to https://github.com/nf-core/sarek

nRex: Germline and somatic single-nucleotide, short indel and structural variant calling

dv-trio provides a pipeline to call variants for a trio (father-mother-child) using DeepVariants [1]. Genomic Variant Calling Files (gVCFs) created by DeepVariants are then co_called together using GATK[2]. The resultant trio VCF is then post-processing with FamSeq[3] to eliminate mendelian errors.

Sentieon Dnascope Ml ⭐ 7

Sentieon DNAscope + Machine Learning Model

Nextflow bioinformatics pipeline for large-scale analysis of Multiple Myeloma genomes

A scalable variant calling and benchmarking framework supporting both short and long reads.

Rmahunter ⭐ 6

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