SHORE Subprograms

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

shore correct4pe finds the most likely mapping of repetitive reads by utilizing paired-end information. While in paired read mapping each read is aligned separately, read pair information can be used to increase the likelihood of an alignment by selecting the paired alignment based on the most likely distance between the pairs.

shore correct4pe starts by estimating the insert size distribution. The upper bound of this distribution is usually very sharp (clones longer than expected seem to be very rare), whereas the lower boundary is more blurred and very small clones can be observed as well. The insert size distribution is then translated into a probability distribution for the observation of a given distance of a pairing (where pairing is defined as the combination of one of the mappings of read 1 with one of the mappings of read 2). All possible combinations of the mappings of both reads of a pair are compared and all pairings with a probability equal to zero are dismissed. Mappings which are not in a pairing with a probability above zero are deleted. This removes all repetitive mappings, which resulted from repeats. If there is a mapping of one read pair with two different mappings of the other read the more likely pairing is kept. If all pairings have zero probability all mappings of both reads are kept. These are the discordant (unhappy) read pairs which typically are used to predict structural variants.

shore correct4pe will plot the insert size distribution using the R if -p is specified. In this case R has to be installed and included in the PATH environment variable.

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