sbptools is a suite of computational pipelines to analyze NGS data.
It is free to use and distribute this software package, but without any warranty.
sbptools version: $version Usage: sbptools [tool] [parameters]
Parameters:
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#Supported in both Firefly and Falco
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rnaseq-process RNA-seq QC, Align, and RSEM for FASTQ files
rnaseq-merge Merge rnaseq-process results for downstream analyses
rnaseq-de Perform DE analysis using DESeq2
rnaseq-summary Summarize RNA-Seq DE results
rnaseq-var RNA-seq variant calling pipeline
rnaseq-motif RNA-seq TFBS motif finding pipeline
rnaseq-motif-summary RNA-seq TFBS motif finding results summary
motif-finder Transcription factor binding motif prediction
chipseq-process ChIP-seq/ATAC-Seq QC, Align, and Peak Calling
chipseq-merge Summarize ChIP-Seq results
chipseq-de Perform DE analysis for ChIP-Seq
chipseq-summary Summarize ChIP-seq DE results
dnaseq-process DNA-Seq (Exome/Genome-Seq) processing based on GATK4
mergefiles Use a model file to merge different files together
text2excel Build excel file using text file (by Andrew Hodges)
gsea-gen Generate files ready for GSEA analysis
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#Supported only in Firefly
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parallel-job Batch job submission in Firefly
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#Supported only in Falco
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bs-fastq Download and merge FASTQ files from Basespace
ensembl2ucsc Convert Ensembl gtf/fasta/bed into UCSC format
geo-download Download raw FASTQ files from GEO