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
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
Eusing Free Registry Cleaner is a free registry repair software that allows you to safely clean and repair registry problems with a few simple mouse clicks.The Windows Registry is a crucial part of your PC's operation system.
This tool uses a unique concentric pie chart to display the usage of your hard disk or other media. The chart shows all major files and folders from all directory levels at once.
How to Remove Windows WMV DRM! All you need is a windows box, a license to play the files, wmp9 and drmdbg or sidda or drmcreep or drm2wmv programs. The dlls and programs and small instructions are included in the link (600k zip). Get more information
To the home of ISO Master: an open-source, graphical CD image editor that runs on Linux; and bkisofs, the underlying library used for reading, modifying and writing ISO images.
To the home of ISO Master: an open-source, graphical CD image editor that runs on Linux; and bkisofs, the underlying library used for reading, modifying and writing ISO images.
Poweroff is a small program for Win95/98/NT/W2K/XP to schedule a shutdown/reboot/logoff/poweroff/Standby/Hibernate/Lock/Wake-On-LAN at a certain time. I also support command line options that allows poweroff to be used in batch scripts. It has a built-in
PathSync - an interactive directory (path) synchronizer for windows PathSync can analyze two directories and show the user a list of differences between the directories. The user can select what actions should occur (which files to overwrite, which to del
PhotoRec is file data recovery software designed to recover lost pictures (Photo Recovery) from digital camera memory and lost files including video, documents and archives from Hard Disks and CDRom. PhotoRec ignores the filesystem and goes after the unde
PhotoRec is file data recovery software designed to recover lost pictures (Photo Recovery) from digital camera memory and lost files including video, documents and archives from Hard Disks and CDRom. PhotoRec ignores the filesystem and goes after the unde
PhotoRec is file data recovery software designed to recover lost files including video, documents and archives from Hard Disks and CDRom and lost pictures (thus, its 'Photo Recovery' name) from digital camera memory. PhotoRec ignores the filesystem and goes after the underlying data, so it will still work even if your media's filesystem has been severely damaged or re-formatted.
Pismo File Mount Audit Package is a Windows application that allows users to mount the contents of ZIP, ISO, Compact ISO, Compact File Set and Private Folder files to the file system as virtual folders.
Safarp is a small and fast alternative to the Add or Remove Programs Control Panel applet of Windows 2000/XP. It displays a list of the installed programs and allows one to uninstall / repair them. Additional features are: * Search function * Obsolete lis
The power to speed up your computer's startup process! Can you learn another language in the time it takes for your machine to boot? Do you turn on your PC when you go to bed, so it's finished booting by the time you get home from work the next day? When
The power to speed up your computer's startup process! Can you learn another language in the time it takes for your machine to boot? Do you turn on your PC when you go to bed, so it's finished booting by the time you get home from work the next day? When
TestDisk is a powerful free data recovery utility! It was primarily designed to help recover lost partitions and/or make non-booting disks bootable again when these symptoms are caused by faulty software, certain types of viruses or human error (such as a
TestDisk is a powerful free data recovery utility! It was primarily designed to help recover lost partitions and/or make non-booting disks bootable again when these symptoms are caused by faulty software, certain types of viruses or human error (such as a
TestDisk ist ein leistungsstarkes freies Daten-Wiederherstellungs-Utility! Es wurde in erster Linie erstellt um verlorene Partitionen wiederherzustellen und/oder nicht bootende Festplatten wieder bootfähig zu machen, wenn das Problem durch fehlerhafte Software, bestimmte Arten von Viren oder menschliche Fehler (wie versehentliches Löschen der Partitionstabelle) verursacht wird. Partitionstabellen wiederherstellen mit TestDisk ist wirklich einfach.
WebSnapr lets you capture screenshots of (almost) any web page. Let your visitors to instantly visualize any web page before clicking. Increase site traffic, click-through rate and site stickiness.
WebSnapr lets you capture screenshots of (almost) any web page. Let your visitors to instantly visualize any web page before clicking. Increase site traffic, click-through rate and site stickiness.