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About FLASHFLASH (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. |
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AccuracyFLASH 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:
Simulated reads used in the experiments are available here: No error 1% error 2% error 3% error 5% error FLASH accuracy on real data:
The reads are available at the GAGE site: Reads from GAGE | ||||||||||||||||||||||
Time requirementsThe latest version of FLASH includes a multi-threaded mode.When run in single threaded mode:
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Impact of FLASH on genome assembliesMerging mate pairs by FLASH as a pre-processor for genome assembly yields singificantly higher N50 value of contigs and scaffolds. It also reduces the number of missassembled contigs. |
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PublicationFLASH: Fast length adjustment of short reads to improve genome assemblies. T. Magoc and S. Salzberg. Bioinformatics 27:21 (2011), 2957-63. |
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Obtaining the SoftwareThis 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:
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Questions/Comments/RequestsSend an e-mail to [email protected]. |
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FundingThis work has been supported in part by NIH grants R01-LM006845, R01-GM083873, and R01-HG006677 to S.L. Salzberg. |