Omictools suite for omics data processing in AWS HPC environment.
omictools
version: $version
Usage: omictools [tool] [parameters]
Parameters:
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#RNA-Seq
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rnaseq-process RNA-seq QC, Align, and Counting for FASTQ files
rnaseq-merge Merge rnaseq-process results for downstream analyses
rnaseq-de Perform DE/AS analyses
rnaseq-summary Summarize RNA-Seq DE results
prepare-merge Generate a merge folder from raw count file for rnaseq-de/summary analysis
rnaseq-var RNA-seq variant calling pipeline
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#ChIP-Seq
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chipseq-process ChIP-seq/ATAC-seq QC, Align, Peak calling and Counting for FASTQ files
chipseq-merge Merge chipseq-process results for downstream analyses
chipseq-de Perform DE analyses for ChIP-seq peaks
chipseq-summary Summarize ChIP-Seq results
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#DNA-Seq
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dnaseq-process WGS/WES variant calling from FASTQ files using GATK workflow
dnaseq-summary Summarize variant calling results
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#AWS
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parallel-job Batch job submission to HPC
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#Data Download
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bs-fastq Download and merge FASTQ files from Basespace
geo-download Download raw FASTQ files from GEO
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#Misc tools
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mergefiles Use a model file to merge different files together
text2excel Build excel file using text file
extract-command Extract a command from omictools script file