Flash Dog !!INSTALL!!
Lee Stlaurent
About FLASH FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data.
Accuracy FLASH merges reads from paired-end sequencing runs with very high accuracy.
FLASH accuracy on one million 100bp long synthetic pairs generated from fragments with a mean length of 180bp, normaly distributed with a standard deviation of 20bp:
No error 1% error rate 2% error rate 3% error rate 5% error rate default parameters 99.73% 99.68% 98.43% 94.76% 77.91% more aggressive parameters 99.73% 99.68% 99.06% 98.30% 93.65%
Simulated reads used in the experiments are available here:
No error
1% error
2% error
3% error
5% error
FLASH accuracy on real data:
647,052 pairs of 101bp long reads from Staphylococcus aureus 90.77% 18,252,400 pairs of 101bp long reads from human 91.02%
The reads are available at the GAGE site: Reads from GAGE Time requirements The latest version of FLASH includes a multi-threaded mode.
When run in single threaded mode:
- FLASH takes 120 seconds to process one million 100-bp long pairs on a server with 256GB of RAM and a six-core 2.4GHz AMD Opteron CPU.
- FLASH takes 129 seconds to process one million 100-bp long pairs on a desktop with 2GB of RAM and a dual-core Intel Xeon 3.00GHz CPU. Time is linearly proportional to the read length and the number of reads.
Publication FLASH: Fast length adjustment of short reads to improve genome assemblies. T. Magoc and S. Salzberg. Bioinformatics 27:21 (2011), 2957-63.
Obtaining the Software This software is OSI Certified Open Source Software.
FLASH code or executable can be downloaded from Sourceforge. Release packages can also be directly downloaded from here:
- source package: FLASH-1.2.11.tar.gz
- precompiled Linux x86_64 binary: FLASH-1.2.11-Linux-x86_64.tar.gz
- precompiled Windows binary: FLASH-1.2.11-windows-bin.zip
Funding This work has been supported in part by NIH grants R01-LM006845, R01-GM083873, and R01-HG006677 to S.L. Salzberg. The Center for Computational Biology at Johns Hopkins University
I use the flash function often to try find features that are searched for in the "Find" tool. The right-click "flash" option would be much more useful if the flash was highly visible, for example have it be large a bright red-yellow-or even blue (as the default for selected features).
My idea then is to be able to change the default for this or make it's much more visible.
ben
Yes, when zoomed out and trying to Flash a tiny shape, it's impossible in Pro to see where the flash occurs. In ArcMap, crosshairs would appear on the screen pinpointing exactly where the shape is on the map.
Flash memory, also known as flash storage, is a type of nonvolatile memory that erases data in units called blocks and rewrites data at the byte level. Flash memory is widely used for storage and data transfer in consumer devices, enterprise systems and industrial applications. Flash memory retains data for an extended period regardless of whether a flash-equipped device is powered on or off.
Flash memory is used in enterprise data center server, storage and networking technology as well as in a wide range of consumer devices, including USB flash drives -- also known as memory sticks -- SD cards, mobile phones, digital cameras, tablet computers, and PC cards in notebook computers and embedded controllers.
There are two types of flash memory: NAND and NOR. NAND flash-based solid-state drives (SSDs) are often used to accelerate the performance of I/O-intensive applications. NOR flash memory is often used to hold control code, such as the BIOS in a PC.
Dr. Fujio Masuoka is credited with inventing flash memory when he worked for Toshiba in the 1980s. Masuoka's colleague, Shoji Ariizumi, reportedly coined the term flash because the process of erasing all the data from a semiconductor chip reminded him of the flash of a camera.
Flash memory evolved from erasable programmable read-only memory (EPROM) to electrically erasable programmable read-only memory (EEPROM). Flash is technically a variant of EEPROM, but the industry reserves the term EEPROM for byte-level erasable memory and applies the term flash memory to larger block-level erasable memory.
Structure. Flash memory architecture includes a memory array stacked with a multitude of flash cells. A basic flash memory cell consists of a storage transistor with a control gate and a floating gate, which is insulated from the rest of the transistor by a thin dielectric material or oxide layer. The floating gate stores the electrical charge and controls the flow of the electrical current.
Electrical isolation and persistent storage. Electrons are trapped in the floating gate regardless of whether a device containing the flash memory cell is receiving power because of electrical isolation created by the oxide layer. This characteristic enables flash memory to provide persistent storage.
NOR and NAND flash memory differ in architecture and design characteristics. NOR flash uses no shared components and can connect individual memory cells in parallel, enabling random access to data. A NAND flash cell is more compact and has fewer bit lines, stringing together floating gate transistors to increase storage density.
NOR flash is fast on data reads, but it's typically slower than NAND on erases and writes. NOR flash programs data at the byte level. NAND flash programs data in pages, which are larger than bytes, but smaller than blocks. For instance, a page might be 4 kilobytes (KB), while a block might be 128 KB to 256 KB or megabytes in size. NAND flash consumes less power than NOR flash for write-intensive applications.
NOR flash is more expensive to produce than NAND flash and tends to be used primarily in consumer and embedded devices for boot purposes and read-only applications for code storage. NAND flash is more suitable for data storage in consumer devices as well as enterprise server and storage systems due to its lower cost per bit to store data, greater density, and higher programming and erase speeds.
An additional subcategory is a hybrid hard drive that combines a conventional HDD with a NAND flash module. A hybrid hard drive is generally viewed to bridge the divide between rotating media and flash memory.
The advent of flash memory fueled the rise of all-flash arrays. These systems, which contain only SSDs, offer advantages in performance and potentially reduced operational costs compared to all disk-based storage arrays. The chief difference, aside from the media, is in the underlying physical architecture used to write data to a storage device.
HDD-based arrays have an actuator arm that lets data be written to a specific block on a specific sector on the disk. All-flash storage systems don't require moving parts to write data. The writes are made directly to the flash memory and custom software handles data management.
A hybrid flash array blends disk and SSDs. Hybrid arrays use SSDs as a cache to speed access to frequently requested hot data, which subsequently is rewritten to back-end disk. Many enterprises commonly archive data from disk as it ages by replicating it to an external magnetic tape library.
In addition to flash memory arrays, the ability to insert SSDs in x86-based servers has increased the technology's popularity. This arrangement is known as server-side flash memory, and it lets companies sidestep the vendor lock-in associated with purchasing expensive and integrated flash storage arrays.
The drawback of placing flash in a server is that users must build the hardware system internally, including the purchase and installation of a storage management software stack from a third-party vendor.
The main disadvantages of flash memory are the wear-out mechanism and cell-to-cell interference as the dies get smaller. Bits can fail with excessively high numbers of program/erase cycles, which eventually break down the oxide layer that traps electrons. The deterioration can distort the manufacturer-set threshold value at which a charge is determined to be a zero or a one. Electrons could escape and get stuck in the oxide insulation layer, leading to errors and bit rot.
Anecdotal evidence suggests NAND flash drives aren't wearing out to the degree once feared. Flash drive manufacturers have improved endurance and reliability through error correction code algorithms, wear leveling and other technologies.
The two main types of NOR flash memory are parallel and serial, also known as serial peripheral interface. NOR flash was originally available only with a parallel interface. Parallel NOR offers high performance, security and additional features. Its primary uses include industrial, automotive, networking and telecom systems and equipment.
Serial NOR flash has a lower pin count and smaller packaging, making it less expensive than parallel NOR. Use cases for serial NOR include personal and ultra-thin computers, servers, HDDs, printers, digital cameras, modems and routers.
Major manufacturers of NAND flash memory chips include Kioxia -- formerly Toshiba Memory Corp. -- Micron Technology Inc., Samsung, SK Hynix Inc. and Western Digital Corp. Intel, which was once a leading chip manufacturer, sold its SSD business in 2020 to SK Hynix.
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