fastq-analysis-pipeline
Overview
OmicVerse provides a complete FASTQ-to-count-matrix pipeline via the ov.alignment module. This skill covers:
- SRA data acquisition:
prefetchandfqdump(fasterq-dump wrapper) - Quality control:
fastpfor adapter trimming and QC reports - RNA-seq alignment:
STARaligner with auto-index building - Gene quantification:
featureCount(subread featureCounts wrapper) - Single-cell path:
refandcountvia kb-python (kallisto/bustools) - Parallel SRA download:
parallel_fastq_dump
All functions share a common CLI infrastructure (_cli_utils.py) that handles tool resolution, auto-installation via conda/mamba, parallel execution, and streaming output.
Instructions
- Environment setup
- Bioinformatics tools are resolved automatically from PATH or the active conda environment.
- If
auto_install=True(default), missing tools are installed via mamba/conda on demand. - Supported tools:
prefetch,vdb-validate,fasterq-dump,fastp,STAR,samtools,featureCounts,pigz,gzip.
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