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