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Search results for genomics variant calling
genomics
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variant-calling
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34 search results found
Jcvi
⭐
650
Python library to facilitate genome assembly, annotation, and comparative genomics
Vcflib
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594
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
Snippy
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408
✂️ ⚡ Rapid haploid variant calling and core genome alignment
Sarek
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299
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Octopus
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285
Bayesian haplotype-based mutation calling
Clair3
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191
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
Viral Ngs
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129
Viral genomics analysis pipelines
Fermikit
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91
De novo assembly based variant calling pipeline for Illumina short reads
Genomicsdb
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88
High performance data storage for importing, querying and transforming variants.
Mccortex
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86
De novo genome assembly and multisample variant calling
Tiledb Vcf
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79
Efficient variant-call data storage and retrieval library using the TileDB storage library.
Callings Nf
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76
GATK RNA-Seq Variant Calling in Nextflow
Dysgu
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75
Toolkit for calling structural variants using short or long reads
Hla
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57
xHLA: Fast and accurate HLA typing from short read sequence data
Vcfdist
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48
vcfdist: Accurately benchmarking phased variant calls
Kevlar
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42
Reference-free variant discovery in large eukaryotic genomes
Balsamic
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40
Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
Indelope
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39
find large indels (in the blind spot between GATK/freebayes and SV callers)
Variantworks
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38
Deep Learning based variant calling toolkit - https://clara-parabricks.github.io/VariantWorks/
Chm Eval
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37
Cerebra
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26
A tool for fast and accurate summarizing of variant calling format (VCF) files
Arcsv
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19
Complex structural variant detection from WGS data
Clairs To
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18
ClairS-TO - a deep-learning method for tumor-only somatic SNV calling
Clair3 Trio
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12
Clair3-Trio: variant calling in trio using Nanopore long-reads
Genome On Diet
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11
Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version: https://arxiv.org/abs/2211.08157).
Exoseq
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10
Please consider using/contributing to https://github.com/nf-core/sarek
Npore
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10
nPoRe: n-Polymer Realigner for improved pileup-based variant calling
Bioinformatics
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10
A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common DNA and RNA sequence analysis methods.
Tbpore
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9
Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
Varathon
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7
A scalable variant calling and benchmarking framework supporting both short and long reads.
Mgp1000
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7
Nextflow bioinformatics pipeline for large-scale analysis of Multiple Myeloma genomes
Snipgenie
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6
command line and desktop tool for microbial variant calling
Nf Ncov Voc
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5
A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 genomes (Variants of Concern and Variants of Interest). Workflow is developed in collaboration with COVID-MVP (https://github.com/cidgoh/COVID-MVP) which can be used to visualize the mutation profiles and functional annotations.
Allmine
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5
AllMine, a flexible pipeline for Allele Mining. Develloped at INRA's GAFL unit :
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1-34 of 34 search results
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