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1 Tool wrapper by Brian Yeo
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2 brian.yeo@phac.aspc.gc.ca
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3
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4 INTRODUCTION
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5
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6 FLASH (Fast Length Adjustment of SHort reads) is an accurate and fast tool
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7 to merge paired-end reads that were generated from DNA fragments whose
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8 lengths are shorter than twice the length of reads. Merged read pairs result
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9 in unpaired longer reads, which are generally more desired in genome
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10 assembly and genome analysis processes.
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11
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12 Briefly, the FLASH algorithm considers all possible overlaps at or above a
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13 minimum length between the reads in a pair and chooses the overlap that
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14 results in the lowest mismatch density (proportion of mismatched bases in
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15 the overlapped region). Ties between multiple overlaps are broken by
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16 considering quality scores at mismatch sites. When building the merged
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17 sequence, FLASH computes a consensus sequence in the overlapped region.
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18 More details can be found in the original publication
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19 (http://bioinformatics.oxfordjournals.org/content/27/21/2957.full).
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20
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21 Limitations of FLASH include:
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22 - FLASH cannot merge paired-end reads that do not overlap.
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23 - FLASH cannot merge read pairs that have an outward orientation, either
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24 due to being "jumping" reads or due to excessive trimming.
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25 - FLASH is not designed for data that has a significant amount of indel
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26 errors (such as Sanger sequencing data). It is best suited for Illumina
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27 data.
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28
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29 INSTALLATION
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30
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31 On UNIX-compatible systems, including GNU/Linux and Mac OS X, you must compile
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32 FLASH from source. The only dependency, other than functions that are expected
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33 to be available in the C library, is the zlib data compression library. To
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34 install FLASH, download the tarball, untar it, and compile the code using the
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35 provided Makefile:
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36
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37 $ tar xzf FLASH-1.2.9.tar.gz
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38 $ cd FLASH-1.2.9
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39 $ make
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40
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41 The executable file that is produced is named 'flash'. To run it from the
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42 command line you must copy it to a location on your $PATH variable, or else run
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43 it with a path including a directory, such as "./flash".
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44
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45 FLASH also runs on Windows, and you can compile it on Windows using MinGW.
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46 However, for convenience you may instead download a standalone Windows binary
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47 from the SourceForge page (https://sourceforge.net/projects/flashpage/).
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48
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49 USAGE
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50
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51 Please compile FLASH and run `flash --help' to see command-line usage
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52 information and information about input/output files.
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53
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54 MULTITHREADING
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55
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56 By default, FLASH uses multiple threads. There are "combiner" threads that do
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57 the actual read combining, as well as up to 5 threads that are used for I/O (up
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58 to 2 readers, up to 3 writers). The default number of combiner threads is the
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59 number of processors; however, it can be adjusted with the -t option (long
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60 option: --threads).
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61
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62 When multiple combiner threads are used, the order of the combined and
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63 uncombined reads in the output files will be nondeterministic. If you need to
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64 enforce that the output reads appear in the same order as the input, you must
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65 specify --threads=1.
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66
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67 PERFORMANCE
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68
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69 Since the FLASH algorithm considers each read pair independently, FLASH will, by
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70 default, process read pairs in parallel. FLASH v1.2.9 and later also make use
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71 of vector instructions available on modern x86 CPUs. Consequently, FLASH works
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72 quite fast, even with low-cost computing resources. As an example, we ran FLASH
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73 v1.2.9 on a laptop with a dual-core 2.3 GHz AMD x86_64 processor and it
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74 processed one million 101-bp read pairs in 11.6 seconds with the default
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75 parameters. Less than 2 MB of memory was used. Actual timing results will
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76 vary, but they will depend primarily on the number of CPUs available, the speed
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77 of each CPU, and on the I/O speed of reading the input files and writing the
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78 output files. FLASH is designed to be scalable to dozens of processors,
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79 although its speed may be limited by I/O in such cases.
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80
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81 ACCURACY
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82
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83 With reads' error rate of 1% or less, FLASH processes over 99% of read pairs
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84 correctly. With error rate of 2%, FLASH processes over 98% of read pairs
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85 correctly when default parameters are used. With more aggressive parameters
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86 (i.e., -x 0.35), FLASH processes over 90% of read pairs correctly even when the
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87 error rate is 5%.
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88
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89 PUBLICATION
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90
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91 Title: FLASH: fast length adjustment of short reads to improve genome assemblies
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92 Authors: Tanja Magoč and Steven L. Salzberg
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93 URL: http://bioinformatics.oxfordjournals.org/content/27/21/2957.full
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94
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95 LICENSE
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96
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97 FLASH is released under the GNU General Public License Version 3 or later (see
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98 COPYING).
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99
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100 COMMENTS/QUESTIONS/REQUESTS
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101
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102 Send an e-mail to flash.comment@gmail.com
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103
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104 Other versions are available from the SourceForge page:
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105
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106 https://sourceforge.net/projects/flashpage/
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