病原微生物高通量测序数据分析笔记

Tools for working with genomic and high throughput sequencing data.

https://www.sc-best-practices.org

Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"

A modular annotation tool for genomic variants

Tool for automated classification of genetic variants according to ACMG criteria.

Variant calling pipeline for amplicon sequencing data

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Generic human DNA variant annotation pipeline

SMN1 copy-number and sequence variant analysis from next generation sequencing data

A Tool to Annotate and Prioritize Exome Variants

Predict fetal fraction from sequenced DNA extracted from maternal blood

multiPrime is a mismatch-tolerant minimal primer set design tool for large and diverse sequences (e.g. Virus). Here is a web-based version (test: http://multiPrime.cn))

web-based analysis tool for rare disease genomics

A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data

This is a pipeline for variant annotation in the diagnosis of rare genetic disorders. It relies on open source data and has instructions for software installs.

This is a modiifed port of the original https://github.com/JiguangPeng/autopvs1, branched from commit `7fb1be97667e5ef576f81bf2fabbddcf9a4c7594`. It was re-worked in order to work with Kids First g…

A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.

ampliCNV is a Python 3.x package for copy number (CNV) variation detection on whole exome sequencing (WES) data from amplicon-based enrichment technologies.

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Fast C code for identifying and removing primers and adapters

VarDict

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

Characterization of Germline variants

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.

A standalone and free application to explore genetics variations from VCF file

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A simple script to create a customizable html file from an AnnotSV output.