Difference between revisions of "SHORE Subprograms"
From SHORE wiki
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|[[shore mg]] || Primitive metagenomic analysis | |[[shore mg]] || Primitive metagenomic analysis | ||
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| − | |[[shore count]] || Gather quantitative information for predefined | + | |[[shore count]] || Gather quantitative information for predefined loci |
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Revision as of 10:52, 28 September 2011
Contents
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 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 |
