Difference: NGSAlignerToDo (1 vs. 5)

Revision 52010-05-20 - jujubix

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META TOPICPARENT name="NGSAlignerProject"

Specifications

Line: 38 to 38
 
  • Have CMake detect CPU architecture and link appropriate libraries
  • Build as "Release" in ccmake for full optimization
Added:
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Miscellaneous Questions

  • Do we ever have to assume that the reference is circular (i.e. how to handle negative and out of range positions)
  • Do we ever have to support positive penalty values?

Revision 42010-04-20 - jujubix

Line: 1 to 1
 
META TOPICPARENT name="NGSAlignerProject"

Specifications

Line: 13 to 13
 
  • Small memory footprint
  • Align against reference with dynamic splice graph
  • Minimize the size of the driver (i.e. abstract functions into classes)
Added:
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  • Feedback loop of discovered SNPs back into reference
 

Read Specific Needs

  • Works with 75bp reads, up to 128bp

Revision 32010-04-14 - jujubix

Line: 1 to 1
 
META TOPICPARENT name="NGSAlignerProject"

Specifications

Line: 8 to 8
 

General Needs

  • Works in letter space with RNA-Seq data
Changed:
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  • Works in colour space with SOLiD data
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  • Works in colour space with SOLiD data
 
  • Fast
  • Small memory footprint
  • Align against reference with dynamic splice graph

Revision 22010-04-12 - jujubix

Line: 1 to 1
 
META TOPICPARENT name="NGSAlignerProject"
Changed:
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NGS Aligner To Do List

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Specifications

 
Changed:
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Features

  • Prevent losing SNPs at the end of reads from clipping
  • Rescue transcriptome reads with huge chunks of mismatched introns
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File Formats

  • Reads input as FASTQ
  • Alignments output as SAM

General Needs

  • Works in letter space with RNA-Seq data
  • Works in colour space with SOLiD data
  • Fast
  • Small memory footprint
  • Align against reference with dynamic splice graph
  • Minimize the size of the driver (i.e. abstract functions into classes)

Read Specific Needs

  • Works with 75bp reads, up to 128bp
  • Rescue transcriptome reads with huge chunks of mismatched introns (e.g. NNNIIIII; I = intron)
 
  • Split transcriptome reads to align across an intron junction
Added:
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>
  • Handle residual introns within exome reads (e.g. NNNIINNN)
  • Handle resitual introns flanking exome reads (i.e. NNNNNNII)
  • Prevent losing SNPs at the end of reads from clipping (e.g. NNNNNXN; N = base; X = SNP)

Alignment Specific Needs

  • User-specified method of handling multimapped reads (i.e. read mapping equally well to multiple positions)
  • Supports extended CIGAR encoding (including P for Padding)
  • Confirm if traceback ever needs to return multiple best alignments
 
Changed:
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Implementation

  • Decide if traceback ever needs to return more than 1 alignment
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Quality Specific Needs

  • Alignment Score (from alignment)
  • Mapping Quality (as defined by MAQ, using Mosaik's implementation)
  • Uniqueness (out of 100%, divided by number best mapped positions)
  • Fragment Quality (PE specific value, probability that mapped fragment (flanked by PE) location is correct/incorrect)
 
Changed:
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Compilation

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Build and Complication

 
  • Have CMake detect CPU architecture and link appropriate libraries
Added:
>
>
  • Build as "Release" in ccmake for full optimization
 

Revision 12010-04-09 - jujubix

Line: 1 to 1
Added:
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META TOPICPARENT name="NGSAlignerProject"

NGS Aligner To Do List

Features

  • Prevent losing SNPs at the end of reads from clipping
  • Rescue transcriptome reads with huge chunks of mismatched introns
  • Split transcriptome reads to align across an intron junction

Implementation

  • Decide if traceback ever needs to return more than 1 alignment

Compilation

  • Have CMake detect CPU architecture and link appropriate libraries
 
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