SHORE Subprograms

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The following is a non-exhaustive list of commands available through the SHORE main program.

Preprocessing the reference sequence

shore preprocess Prepares index files, local repeat and gc content files from reference sequence

Preparing and filtering read data

shore import Prepare short read data for processing

Short read alignment

shore mapflowcell Short read mapping
shore correct4pe Improves mapping using paired-end information
shore merge Merges and filters alignment files
shore mapdisp Text-based alignment visualization


shore consensus Computes consensus sequence, SNPs, indels and CNVs from alignments (legacy version)
shore qVar Computes consensus sequence, SNPs, indels and CNVs from alignments
shore structure Detect structural variants
shore peak ChIP-seq peak detection
shore srna Small RNA analysis
shore coverage Coverage analysis and segmentation
shore mg Primitive metagenomic analysis
shore methyl Quantify methylated and unmethylated cytosines from BS-seq alignments
shore count Gather quantitative information for predefined loci


shore tagstats Gather read statistics for multiple samples
shore binom_test Compares two sets of read counts using a binomial test
shore mtc Generic multiple testing correction
shore ranksim Rankproduct / ranksum simulator
shore annotate_region Relate loci to annotation


shore convert Convert SHORE files into common file formats, and vice versa
shore sort Sort, merge or query tab-delimited text files
shore compress Compress files to indexed gzip format
shore 2dex Range-indexing and query for tab-delimited text files
shore idtrans Translate SHORE sequence IDs into sequence names, and vice versa