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Search results for python variant calling

variant-calling x

29 search results found

Python library to facilitate genome assembly, annotation, and comparative genomics

PEPPER-Margin-DeepVariant

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

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.

Clairvoyante ⭐ 142

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

Viral Ngs ⭐ 129

Viral genomics analysis pipelines

Gramtools ⭐ 90

Genome inference from a population reference graph

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.

Tiledb Vcf ⭐ 79

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

Grenepipe ⭐ 75

A flexible, scalable, and reproducible pipeline to automate variant calling from sequence reads.

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

Balsamic ⭐ 40

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

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

Complex structural variant detection from WGS data

Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.

Clairs To ⭐ 18

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

rMETL - realignment-based Mobile Element insertion detection Tool for Long read

Clair3 Trio ⭐ 12

Clair3-Trio: variant calling in trio using Nanopore long-reads

nPoRe: n-Polymer Realigner for improved pileup-based variant calling

Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data

Snvcallingworkflow ⭐ 7

The DKFZ-ODCF, formerly DKFZ/eilslabs SNV-Calling Workflow

Strainflye ⭐ 7

Pipeline for analyzing (rare) mutations in metagenome-assembled genomes

Snipgenie ⭐ 6

command line and desktop tool for microbial variant calling

Process raw haplotagging data, from raw sequences to phased haplotypes, batteries included.

AllMine, a flexible pipeline for Allele Mining. Develloped at INRA's GAFL unit :

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.

Variant Calling At Scale ⭐ 5

Scalable and High Performance Variant Calling on Cluster Environments

Clair3 Rna ⭐ 5

Clair3-RNA - long-read short variant caller for RNA sequencing data

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