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, 12:22, 8 April 2010
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| == Sequence Analysis Tools == | | == Sequence Analysis Tools == |
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− | We are developing several tools for the analysis of next generation sequence data. | + | We are developing [[Software]] for the analysis of next generation sequence data. |
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− | === [[Read Mapping]] ===
| + | # Read Mapping with [[Karma]] |
− | | + | # Variant Calling with [[glfSingle]], [[glfTrio]] and [[glfMultiples]] |
− | [[Karma|Karma]] - Our fast short read aligner, which generates [[Mapping Quality Scores]]
| + | # Variant Annotations using [[vcfCodingSnps]] |
− | | + | # Quality control using [[FastQValidator]], and [[BamIdentityCheck]] |
− | [[Karma-colorspace|Karma-ColorSpace]] - QUICKSTART on mapping color space reads | + | # File Readers using [[C++ Library: libbam|BamFile]] and [[C++ Library: libfqf|FastQFile]] |
− | | + | # File Conversions using [[bam2FastQ]] |
− | [[Examples|Examples]] - Sample command lines with discussion
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− | [[MapabilityScores]] - Definitions of various mappability scores adopted at UCSC genome browser.
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− | === Variant Calling ===
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− | [[glfSingle]] - Variant calling for a single, deeply sequenced individual | |
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− | [[glfTrio]] - Variant calling for a single, deeply sequenced nuclear family with two parents and one child | |
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− | [[glfMultiples]] -- Variant calling for multiple, unrelated individuals | |
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− | === Variant Annotation ===
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− | [[vcfCodingSnps]] -- Annotate coding variants in a VCF file. | |
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− | === Quality Control Utilities ===
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− | [[C++ Executable: fastQValidator|FastQValidator]] -- Check that a FASTQ file conforms to specification. | |
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− | [[BamIdentityCheck]] -- Check that mapped reads are consistent with known genotypes for each individual. | |
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− | === File Readers ===
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− | [[C++ Library: libbam|BamFile]] -- Reads a BAM/SAM file. | |
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− | [[C++ Library: libfqf|FastQFile]] -- Read a FASTQ file sequence by sequence. Validating the sequence as it is read. | |
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− | === File Conversion ===
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− | [[bam2FastQ]] -- Convert BAM files into FastQ files | |
− | === [[Links to Sequence Analysis Tools|Other Useful Links]] ===
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| == Projects == | | == Projects == |