The program ‘sff2fastq‘ extracts read information from a SFF file,produced by the 454 genome sequencer, and outputs the sequences and quality scores in a FASTQ format.
junction2BED converts the reads supporting junctions from the evidenceJunctionDnbsBeta-[ASM-ID].tsv.bz file (located in the SV directory) to BED format.
Engauge Digitizer converts an image file showing a graph or map, into numbers. The image file can come from a scanner, digital camera or screenshot. The numbers can be read on the screen, and written or copied to a spreadsheet.
CNGen is a scritp that converts integrated SNP and CNV calls generated from Birdsuite ‘s Fawkes procedure into phased copy number genotypes (CN genotypes) using familial pedigree data. This software makes possible the use of CNPs and CNVs for genetic linkage with family data.
TABLE takes the output from MLINK or LINKMAP and tabulates it in a more easily digestible form. It can also produce files suitable for graphing lod scores and for input to HOMOG, BTEST and FASTMAP.
PyMsXML is a python script for converting vendor specific mass spectrometry data files for Applied Biosystems’ Q-Star, 4700, 4800, Mariner, and Voyager mass spectrometers from their raw binary form, to either of the emerging XML file formats for mass spectra: mzXML, from the Sashimi Glossolalia project of the Institute for Systems Biology (ISB); and mzData, from the Proteome Standardization Initiative (PSI) project of the Human Proteome Organization (HUPO).