Difference between revisions of "SHORE Subprograms"
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| + | The following is a non-exhaustive list of commands available through the [[SHORE main program]]. | ||
| + | ===Preprocessing the reference sequence=== | ||
| + | |||
| + | {|cellpadding=5 | ||
| + | |-- | ||
| + | |[[shore preprocess]] || Prepares index files, local repeat and gc content files from reference sequence | ||
| + | |-- | ||
| + | |} | ||
| + | |||
| + | ===Preparing and filtering read data=== | ||
| + | |||
| + | {|cellpadding=5 | ||
| + | |-- | ||
| + | |[[shore import]] || Prepare short read data for processing | ||
| + | |-- | ||
| + | |} | ||
| + | |||
| + | ===Short read alignment=== | ||
| + | |||
| + | {|cellpadding=5 | ||
| + | |-- | ||
| + | |[[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=== | ||
| + | |||
| + | {|cellpadding=5 | ||
| + | |-- | ||
| + | |[[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 methyl]] || Quantify methylated and unmethylated cytosines from BS-seq alignments | ||
| + | |-- | ||
| + | |[[shore count]] || Gather quantitative information for predefined loci | ||
| + | |-- | ||
| + | |} | ||
| + | |||
| + | ===Utilities=== | ||
| + | |||
| + | {|cellpadding=5 | ||
| + | |-- | ||
| + | |[[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 | ||
| + | |-- | ||
| + | |} | ||
| + | |||
| + | ===Tools=== | ||
| + | |||
| + | {|cellpadding=5 | ||
| + | |-- | ||
| + | |[[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 | ||
| + | |-- | ||
| + | |} | ||
Latest revision as of 11:07, 20 June 2013
The following is a non-exhaustive list of commands available through the SHORE main program.
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 methyl | Quantify methylated and unmethylated cytosines from BS-seq alignments |
| shore count | Gather quantitative information for predefined loci |
Utilities
| 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 |
Tools
| 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 |
