Revision as of 14:38, 15 July 2011

shore preprocess

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

shore import

Prepare short read data for processing

shore mapflowcell

Short read mapping

shore correct4pe

Improves mapping using paired-end information

shore merge

Merges and filters alignment files

shore mapview

Text-based alignment visualization

shore consensus

Creates consensus sequence from alignments (legacy version)

shore qVar

Computes consensus sequence, SNPs, indels and CNVs from alignments

shore methyl

Quantify methylated and unmethylated cytosines from BS-seq alignments (only genomemapper)

shore coverage

Coverage analysis and segmentation

shore peak

ChIP-seq peak detection

shore srna

Small RNA analysis

shore tagstats

Gather read statistics for multiple samples without a reference sequence

shore structure

Detect structural variants

shore count

Count reads

shore binom_test

Compares two sets of read counts using a binomial test

shore mtc

Generic multiple testing correction

shore annotate_region

Relate loci to annotation

shore convert

Convert SHORE files into common file formats, and vice versa

shore sort

Sort / merge 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