-
Notifications
You must be signed in to change notification settings - Fork 12
Flash2 has some improvements from flash_1 including new logic from innie and outie overlaps as well as some initial steps for flash for amplicons
License
dstreett/FLASH2
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Folders and files
Name | Name | Last commit message | Last commit date | |
---|---|---|---|---|
Repository files navigation
INTRODUCTION FLASH (Fast Length Adjustment of SHort reads) is an accurate and fast tool to merge paired-end reads that were generated from DNA fragments whose lengths are shorter than twice the length of reads. Merged read pairs result in unpaired longer reads, which are generally more desired in genome assembly and genome analysis processes. Briefly, the FLASH algorithm considers all possible overlaps at or above a minimum length between the reads in a pair and chooses the overlap that results in the lowest mismatch density (proportion of mismatched bases in the overlapped region). Ties between multiple overlaps are broken by considering quality scores at mismatch sites. When building the merged sequence, FLASH computes a consensus sequence in the overlapped region. More details can be found in the original publication (http://bioinformatics.oxfordjournals.org/content/27/21/2957.full). Limitations of FLASH include: - FLASH cannot merge paired-end reads that do not overlap. - FLASH is not designed for data that has a significant amount of indel errors (such as Sanger sequencing data). It is best suited for Illumina data. INSTALLATION On UNIX-compatible systems, including GNU/Linux and Mac OS X, you must compile FLASH from source. The only dependency, other than functions that are expected to be available in the C library, is the zlib data compression library. To install FLASH, download the tarball, untar it, and compile the code using the provided Makefile: $ tar xzf FLASH-1.2.11.tar.gz $ cd FLASH-1.2.11 $ make The executable file that is produced is named 'flash'. To run it from the command line you must copy it to a location on your $PATH variable, or else run it with a path including a directory, such as "./flash". FLASH also runs on Windows, and you can compile it on Windows using MinGW. However, for convenience you may instead download a standalone Windows binary from the SourceForge page (https://sourceforge.net/projects/flashpage/). USAGE Please compile FLASH and run `flash --help' to see command-line usage information and information about input/output files. MULTITHREADING By default, FLASH uses multiple threads. There are "combiner" threads that do the actual read combining, as well as up to 5 threads that are used for I/O (up to 2 readers, up to 3 writers). The default number of combiner threads is the number of processors; however, it can be adjusted with the -t option (long option: --threads). When multiple combiner threads are used, the order of the combined and uncombined reads in the output files will be nondeterministic. If you need to enforce that the output reads appear in the same order as the input, you must specify --threads=1. PERFORMANCE Since the FLASH algorithm considers each read pair independently, FLASH will, by default, process read pairs in parallel. FLASH v1.2.9 and later also make use of vector instructions available on modern x86 CPUs. Consequently, FLASH works quite fast, even with low-cost computing resources. As an example, we ran FLASH v1.2.9 on a laptop with a dual-core 2.3 GHz AMD x86_64 processor and it processed one million 101-bp read pairs in 11.6 seconds with the default parameters. Less than 2 MB of memory was used. Actual timing results will vary, but they will depend primarily on the number of CPUs available, the speed of each CPU, and on the I/O speed of reading the input files and writing the output files. FLASH is designed to be scalable to dozens of processors, although its speed may be limited by I/O in such cases. ACCURACY With reads' error rate of 1% or less, FLASH processes over 99% of read pairs correctly. With error rate of 2%, FLASH processes over 98% of read pairs correctly when default parameters are used. With more aggressive parameters (i.e., -x 0.35), FLASH processes over 90% of read pairs correctly even when the error rate is 5%. PUBLICATION Title: FLASH: fast length adjustment of short reads to improve genome assemblies Authors: Tanja Magoč and Steven L. Salzberg URL: http://bioinformatics.oxfordjournals.org/content/27/21/2957.full LICENSE FLASH is released under the GNU General Public License Version 3 or later (see COPYING). MODIFICATIONS Modications that were undertook: -Outies logic was changed Over lap was still Allgined like this. . . <-------------- Read 1 --------------> Read 2 But This was not kept, the overlapping area was kept ------ Read 1 ------ Read 2 -"Engulf" Case was added -If read 2 (or read 1) was engulfed by the other - they would not overlap -This allows for that to be an overlap - along with a new argument min-overlap-outie -"Threshold Quality" was added -There was some significant problems with primer dimers - this removed most of them -This is one of the first steps for flashdbcamp. COMMENTS/QUESTIONS/REQUESTS Send an e-mail to streett.david@gmail.com for information on the modified flash2 Original unmodified version is available from the SourceForge page: https://sourceforge.net/projects/flashpage/
About
Flash2 has some improvements from flash_1 including new logic from innie and outie overlaps as well as some initial steps for flash for amplicons
Resources
License
Stars
Watchers
Forks
Packages 0
No packages published