Sequence alignment data is often ordered by coordinate (id of the reference sequence plus position on the sequence where the fragment was mapped) when stored in BAM files, as this simplifies the extraction of variants between the mapped data and the reference or of variants within the mapped data. In this order paired reads are usually separated in the file, which complicates some other applications like duplicate marking or conversion to the FastQ format which require to access the full information of the pairs. In this paper we introduce biobambam, a set of tools based on the efficient collation of alignments in BAM files by read name. The employed collation algorithm avoids time and space consuming sorting of alignments by read name where this is possible without using more than a specified amount of main memory. Using this algorithm tasks like duplicate marking in BAM files and conversion of BAM files to the FastQ format can be performed very efficiently with limited resources. We also make the collation algorithm available in the form of an API for other projects. This API is part of the libmaus package. In comparison with previous approaches to problems involving the collation of alignments by read name like the BAM to FastQ or duplication marking utilities our approach can often perform an equivalent task more efficiently in terms of the required main memory and run-time. Our BAM to FastQ conversion is faster than all widely known alternatives including Picard and bamUtil. Our duplicate marking is about as fast as the closest competitor bamUtil for small data sets and faster than all known alternatives on large and complex data sets.
CurrPorts displays the list of all currently opened TCP/IP and UDP ports on your local computer. For each port in the list, information about the process that opened the port is also displayed, including the process name, full path of the process, version
Darik's Boot and Nuke ("DBAN") is a self-contained boot floppy that securely wipes the hard disks of most computers. DBAN will automatically and completely delete the contents of any hard disk that it can detect, which makes it an appropriate utility for
Darik's Boot and Nuke ("DBAN") is a self-contained boot floppy that securely wipes the hard disks of most computers. DBAN will automatically and completely delete the contents of any hard disk that it can detect, which makes it an appropriate utility for
Disk fragmentation leads to system slowdowns, PC crashes, slow startup and shutdown and sometimes to system failures. Auslogics Disk Defrag® is designed for fast optimization of today's modern hard disks. Get the maximum performance out of your expensive