fastq-analysis-pipeline

Name: fastq-analysis-pipeline
Rating: 5 (1 reviews)
Author: bg-szy

Guide through omicverse's alignment module for SRA downloading, FASTQ quality control, STAR alignment, gene quantification, and single-cell kallisto/bustools pipelines covering both bulk and single-cell RNA-seq workflows.

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Updated 15 days ago

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Overview

OmicVerse provides a complete FASTQ-to-count-matrix pipeline via the ov.alignment module. This skill covers:

SRA data acquisition: prefetch and fqdump (fasterq-dump wrapper)
Quality control: fastp for adapter trimming and QC reports
RNA-seq alignment: STAR aligner with auto-index building
Gene quantification: featureCount (subread featureCounts wrapper)
Single-cell path: ref and count via kb-python (kallisto/bustools)
**Parallel SRA d

[Description truncada. Veja o README completo no GitHub.]

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