Difference between revisions of "SHORE Subprograms"
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=shore import= | =shore import= | ||
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| + | 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= | =shore mapflowcell= | ||
Revision as of 15:14, 15 July 2011
Contents
- 1 shore preprocess
- 2 shore import
- 3 shore mapflowcell
- 4 shore correct4pe
- 5 shore merge
- 6 shore mapview
- 7 shore consensus
- 8 shore qVar
- 9 shore methyl
- 10 shore coverage
- 11 shore peak
- 12 shore srna
- 13 shore tagstats
- 14 shore structure
- 15 shore count
- 16 shore binom_test
- 17 shore mtc
- 18 shore annotate_region
- 19 shore convert
- 20 shore sort
- 21 shore compress
- 22 shore 2dex
- 23 shore idtrans
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
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
