fastp 开源项目推荐（34 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。

UPHL-BioNGS /Donut_Falls

Assembly of Nanopore Sequencing

refmyoussef-source /rnaseq_klebsiella_pipeline

A complete bioinformatics pipeline (FastQC, fastp, HISAT2, featureCounts, DESeq2) for RNA-Seq DGE analysis of Klebsiella pneumoniae (WT vs. ΔcpxR).

srh-bzd /ViroScan-nf

Nextflow pipeline for separating host and viral reads and identifying viral mutations from sequencing data.

shreejan-v /dna-seq-variant-calling-pipeline

End-to-end DNA sequencing variant calling and functional annotation pipeline using FastQC, fastp, BWA-MEM, SAMtools, Picard, GATK HaplotypeCaller, and Ensembl VEP on human NGS datasets.

THEKINGSTAR /capstone_Bactiral_Genomics

A reproducible Whole Genome Sequencing (WGS) quality-control pipeline for Bacterial Genomics using FastQC, MultiQC, and fastp.

OpenOmics /weave

An awesome BCL demultiplexing and FastQ quality-control pipeline

muhammetozcelik /genomqc-rnaseq-qc

Reproducible quality control and preprocessing for paired-end RNA-seq FASTQ files

hafizmtalha /TrimView

Interactive FastQC-style quality control and read trimming for FASTQ files: drag to trim, see the exact fastp command, compare before and after. Windows (TrimView.exe), macOS, Linux.

lujdavila-prog /Nextflow-Staph-V1

Single-sample Nextflow DSL2 workflow for FASTQ preprocessing, reference alignment, BAM processing, and alignment QC.

carmengmz /circrna-

Classification of RNA-Seq samples using circRNA expression

sarvezh1 /rna-seq-pipeline

A reproducible RNA-seq analysis pipeline built with Nextflow and Docker, supporting QC, alignment, quantification, differential expression, transcript discovery, and automated reporting.

saumyasingh857 /NGS-QC-Pipeline

NGS Quality Control Pipeline using FastQC, Fastp, and MultiQC for Illumina paired-end sequencing data.

Mynamemd /WES-Analysis-Nextflow

Tumor-normal variant analysis workflow using Nextflow DSL2, FastQC, Fastp, BWA, GATK, ANNOVAR and IGV visualization.

minos1232 /airway-rnaseq

End-to-end RNA-seq differential expression pipeline (fastq-dump → fastp → Salmon → PyDESeq2) analyzing dexamethasone treatment effects in airway smooth muscle cells, with PCA, volcano plots, and pathway enrichment analysis.

Fazizzz /Low-Compute-SingleCell-QC-Nextflow-Pipeline

Low-compute Nextflow pipeline for single-cell RNAseq QC using pseudo-alignment. Two-mode design: with laptop-friendly quick mode for QC and cost prediction, HPC/cloud full mode for Cell Ranger comparable results. Validated on Element AVITI and Illumina NextSeq 2000 sequencing data using 10X V3 Chromium chemistry. Outputs feed scanpy/Seurat directly

2tzntthsd2-star /M_leprae_AMR_pipeline

Automated NGS pipeline for Mycobacterium leprae antimicrobial resistance prediction using BWA, SAMtools, BCFtools and snpEff

alperen-korkmaz-57 /seqc2-panel-variant-analysis

Germline variant calling pipeline (bwa, samtools, bcftools, SnpEff) for targeted cancer panel data from the public SEQC2 reference sample, with an R/Quarto report.

pommevilla /snakemake-genome-assembly-practice

该项目在 GitHub 上没有填写描述

erudite-shreya21 /sars_cov2_variant_calling_pipeline

Hands-on implementation of a SARS-CoV-2 variant calling pipeline using NGS data and Linux-based bioinformatics tools.