SHORE Subprograms

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

Analysis

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

Utility

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