shore preprocess

shore preprocess creates the mapping indices, calculates local GC content and sequence complexity. In addition, SHORE will create a new copy of the fasta file of the reference sequence featuring adjusted chromosome/contig ids and write all files to the IndexFolder.

shore import

This program converts Illumina GAPipeline BUSTARD directories, FASTQ files or SOLiD csfasta files into SHORE format. shore import will create the necessary files and directory structure.

Input formats of the importer are specified using option -v. Available importers are:

Bustard: Input generated by the GAPipeline (bustard/goat) or SCS programs.
Fastq: FastQ files. Some users prefer Illumina fastq files as standard output from the GAPipeline.
Solid: SOLiD F3 and R3 csfasta and (optionally) QV files.
Shore: SHORE reads_0.fl files. This importer can be used to re-filter or trim reads which are already in SHORE format. In addition, 454 SFF files will also be accepted by this importer.

shore mapflowcell

This program performs the actual read alignments to a reference genome.

SHORE supports various mapping tools to always provide the best option for various applications. The default tool, GenomeMapper, is extensively tested. Currently the other available options are BWA, Bowtie, Novocraft and Eland.

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

SHORE Subprograms

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