64 Open source projects that are alternatives of or similar to sentieon-dnaseq

A handy variant calling pipeline generator for whole genome re-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.

Highly performant data storage in C++ for importing, querying and transforming variant data with C/C++/Java/Spark bindings. Used in gatk4.

Distribution of TEs and their relationship to genes in host genome

find large indels (in the blind spot between GATK/freebayes and SV callers)

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

A bioinformatics pipeline to analyze mtDNA from NGS data

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

💾 📃 "Reads to report" for public health and clinical microbiology

dysgu-SV is a collection of tools for calling structural variants using short or long reads

<<------ Use SnapATAC!!

All about acceleration and compression of Deep Neural Networks

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

GREIN : GEO RNA-seq Experiments Interactive Navigator

Riverbed Community Toolkit is a public toolkit for Riverbed Solutions engineering and integration

Bioinformatics curated workflows that use Biocontainers tools

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Exome/Capture/RNASeq Pipeline Implementation using snakemake

The first app for Mobile DNA Sequence Alignment and Analysis

Fast and accurate gene fusion detection from RNA-Seq data

Bystro genetic analysis (annotation, filtering, statistics)

Finds SNP sites from a multi-FASTA alignment file

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

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

Genomics using open source tools, running on GCP or AWS

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

Pandas ExtensionDtypes for dealing with genomics data

Build and maintain multiple custom conda environments all in once place.

pytorch realtime multi person keypoint estimation

A modular annotation tool for genomic variants

The Kria Robotics Stack (KRS) is a ROS 2 superset for industry, an integrated set of robot libraries and utilities to accelerate the development, maintenance and commercialization of industrial-grade robotic solutions while using adaptive computing.

Complex structural variant detection from WGS data

A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

Assembling the cause of phenotypes and genotypes from NGS data

Improve the quality of a denovo assembly by scaffolding and gap filling

An autonomous parallel processing engine for the browser.

Learning the Variant Call Format

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

A Snakemake workflow to process single samples or cohorts of paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.

Whole Exome/Whole Genome Sequencing alignment pipeline

PEPPER-Margin-DeepVariant

[MLSys 2021] IOS: Inter-Operator Scheduler for CNN Acceleration

Population-wide Deletion Calling

🖱 The mouse and trackpad utility for Mac.

Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files

A reading list for deep graph learning acceleration.

Faster BWA-MEM2 using learned-index

Predict plasmids from uncorrected long read data

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

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

Real-time species-typing visualisation for nanopore data.

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

Experimental VP9 codec support for vdpau-va-driver (NVIDIA VDPAU-VAAPI wrapper) and chromium-vaapi

Python toolkit for building restartable pipelines

A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

Ploidy agnostic phasing pipeline and algorithm

Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set

Multilocus sequence typing by blast using the schemes from PubMLST