freebayes 开源项目推荐（20 个）

digo4 /Clinical-Genomics

这里我们将讨论使用 GATK 最佳实践流程对人类数据集进行变异检测。

USDA-VS /vSNP

vSNP -- validate SNPs

isugifNF /polishCLR

A nextflow pipeline for polishing CLR assemblies

USDA-VS /vSNP3

vSNP -- validate SNPs

brwnj /freebayes-nf

a better freebayes-parallel

tycheleturner /exome_class

Codes for exome sequencing class being taught by Tychele N. Turner, Ph.D.

laura-budurlean /SV-calling-with-SpeedSeq

A workflow for using SpeedSeq to align and call SVs from WGS data

hafizmtalha /SDRscan

Identify sex chromosomes and the sex-determining region (XY/ZW) from male and female whole-genome sequencing, for any ploidy.

biodata-fun /course_material

This directory contains material that I've used in different courses

GiacomoPogliana /Genomics-Project

Automated Bash pipeline for variant analysis in family trio. From raw FASTQ to VCFs. Supports Mendelian inheritance models (AR, de novo, AD) using Bowtie2, FreeBayes, Bedtools and BCFtools. Includes integrated QC reports (FastQC, Qualimap, MultiQC).

CarolinaPB /WUR_mapping-variant-calling

Short read mapping and variant calling

PulmonomicsLab /mcdr-mtb-standalone-v2

Multi-class classification of drug resistance in MTB clinical isolates

Daneshpajouh /callbench

Snakemake workflow that calls germline small variants with bcftools and FreeBayes and benchmarks them against GIAB HG002 with RTG vcfeval, by difficult-region stratum.

petrykalukash-hash /wes-cvid-iei-galaxy-analysis

Reproducible Galaxy-based diagnostic-style WES analysis of public SRA samples focused on CVID/IEI-associated genes.

ftugberk /BSA-QTL-Mapping-Drosophila-Ananassae

BSA-QTL Mapping in Drosophila Ananassae

gmboowa /mtb-mixed-infection-pipeline

mtb-mixed-infection-pipeline enables detection of mixed Mycobacterium tuberculosis infections using a reproducible workflow that integrates Snippy, FreeBayes (pooled mode) & MixInfect2. It processes raw reads through alignment, variant calling & statistical analysis to identify mixed-strain infections

AriannaRigamonti /Genomics

Pipeline for automated genomic variant analysis in inherited diseases, integrating alignment, variant calling, and quality control

Mehwish55 /End-to-End-Variant-Calling-Pipeline-using-Snakemake-NGS-Data-Analysis-Workflow-

Reproducible variant calling pipeline using Snakemake, processing real NGS data from raw FASTQ files to final VCF output with QC, alignment, and variant detection.

PulmonomicsLab /mcdr-mtb-standalone

Multi-class classification of drug resistance in MTB clinical isolates

cnr-ibba /nf-resequencing-mem

Nextflow resequencing pipeline with bwa-mem and freebayes