fastqc

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

sequana pipeline to perform parallel fastqc and summarize results with multiqc plot

Python code to compute adatper content in reads, kmer content, per-base-GC content (at a specific position in a read alignment, against reference genome), per base NC content (at a specific position in a read alignment against the reference genome), per base seq quality (across aligned reads), per base sequence content, per base quality scores, …

Estimate fastq-formatted read abundace in RNA-Seq analysis with Kallisto

Map and post-process your bams for SNP calling

This is a Flask-based web application for generating quality control (QC) reports for Next-Generation Sequencing (NGS) data. Users can upload NGS files and receive a detailed QC report through an intuitive interface for easy data submission and visualization.

A workflow automation script: demultiplex the library sequence, run quality checks, deliver to processing and archiving to NIRD

A Snakemake Workflow for using PolyA_DB and UCSC LiftOver with CellRanger

Professional MCP server for FastQC and MultiQC quality control analysis with advanced visualization and report parsing

Snakemake workflow for Salmon quantification and FastQC quality controls

Bioinformatics workflow platform skeleton with FastAPI, PostgreSQL metadata tracking, and a minimal Nextflow DSL2 FastQC/MultiQC QC workflow.

A Snakemake workflow for quality control assessment of Illumina NGS data using FastQC and MultiQC

A python package for working with inputs to and outputs from the toil-rnaseq pipeline

Standard RNAseq analysis pipeline using snakemake.

Identify genomic variants from raw sequencing data and match them to FDA-approved drugs using Nextflow + Docker. Produces an interactive Streamlit clinical report.

Count your fastq-formatted rna-seq reads with Salmon

Perform basic QC over sequenced data

Tools to analyze fasta or fastaq files with python.

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

Execution-capable genomics workflow agent for reproducible NGS QC, variant-QC, nf-core orchestration, provenance, and agentic reporting.