Genomic Software/Algorithms

Notes for myself on analysis software/algorithms to explore (from ASHG talks and poster sessions):

Aligner

• Karma
• Mosaik

SNP/INDEL Calling

• GigaBayes SNP/short indel caller (Marth Lab, Boston College).  Used in one of the 1000 Genome pipelines (NCBI?)
• ATLAS-Indel2

Structural Variation

• BreakSeq
• Genome STRiP (2,3)

Variant Annotation

• Marvel (Otto Valladares, UPenn)
• VARp Drive (???)
• MutaREPORTER

Sequence Viewer

• Gambit Viewer

Sequence Assembly

• SOAPdenovo
• CORTEX assembler (1, 2, 3)
  

Imputation (see http://bioinformatics.oxfordjournals.org/content/25/11/1449.full)

• Plink (http://pngu.mgh.harvard.edu/~purcell/plink/)
• Merlin (http://www.sph.umich.edu/csg/abecasis/Merlin)
• IMPUTE (http://www.stats.ox.ac.uk/∼marchini/software/gwas/impute.html)
• MACH (http://www.sph.umich.edu/csg/abecasis/MaCH/)
• BEAGLE (http://faculty.washington.edu/browning/beagle/beagle.html)
• fastPhase (http://depts.washington.edu/ventures/UW_Technology/Express_Licenses/fastPHASE.php)

 Pipeline/Analysis

• NCBI genome workbench
• CIDRSeq Suite (not publicly available)

For reference, we use the following currently

• bfast
• bwa
• novoalign
• samtools
• picard
• SVA (minimally)
• GATK
• SeattleSeq