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Search results for bioinformatics variant calling
bioinformatics
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variant-calling
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33 search results found
Jcvi
⭐
650
Python library to facilitate genome assembly, annotation, and comparative genomics
Snippy
⭐
408
✂️ ⚡ Rapid haploid variant calling and core genome alignment
Sarek
⭐
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
Clairvoyante
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142
Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
Fermikit
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91
De novo assembly based variant calling pipeline for Illumina short reads
Gramtools
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90
Genome inference from a population reference graph
Ilus
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89
A handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.
Genomicsdb
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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
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76
GATK RNA-Seq Variant Calling in Nextflow
Dysgu
⭐
75
Toolkit for calling structural variants using short or long reads
Clair
⭐
74
Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling
Vcfdist
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48
vcfdist: Accurately benchmarking phased variant calls
Balsamic
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40
Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
Ococo
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39
Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.
Chm Eval
⭐
37
Popdel
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32
Population-wide Deletion Calling
Gatk4_best_practice
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18
GATK4 Best Practice Nextflow Pipeline
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
Workshop Ngsintro
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12
Workshop • Intro to Bioinformatics using NGS data • 5 days
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).
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.
Exoseq
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10
Please consider using/contributing to https://github.com/nf-core/sarek
Tbpore
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9
Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
Strainflye
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7
Pipeline for analyzing (rare) mutations in metagenome-assembled genomes
Mgp1000
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7
Nextflow bioinformatics pipeline for large-scale analysis of Multiple Myeloma genomes
Harpy
⭐
6
Process raw haplotagging data, from raw sequences to phased haplotypes, batteries included.
Snipgenie
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6
command line and desktop tool for microbial variant calling
Nf Ncov Voc
⭐
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.
Lofreq Fpga
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5
FPGA Acceleration for the LoFreq variant caller
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1-33 of 33 search results
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