Advance Access publication September 7, 2011 | Tanja Magoč* and Steven L. Salzberg
The article introduces FLASH (Fast Length Adjustment of SHort reads), a computational tool designed to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. The authors tested FLASH on simulated data and real-world datasets, demonstrating its high accuracy and speed. FLASH correctly extended and merged reads with an error rate of less than 1% and over 90% of the time even with up to 5% error rates. When used as a pre-processor for genome assemblies, FLASH significantly improved the quality of assemblies, particularly in terms of contig and scaffold N50 lengths. The tool is implemented in C and is freely available as open-source code. The authors also discuss the impact of different parameters on the accuracy of read merging and the challenges posed by tandem repeats. Overall, FLASH is a valuable tool for enhancing the quality of genome assemblies by extending short reads.The article introduces FLASH (Fast Length Adjustment of SHort reads), a computational tool designed to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. The authors tested FLASH on simulated data and real-world datasets, demonstrating its high accuracy and speed. FLASH correctly extended and merged reads with an error rate of less than 1% and over 90% of the time even with up to 5% error rates. When used as a pre-processor for genome assemblies, FLASH significantly improved the quality of assemblies, particularly in terms of contig and scaffold N50 lengths. The tool is implemented in C and is freely available as open-source code. The authors also discuss the impact of different parameters on the accuracy of read merging and the challenges posed by tandem repeats. Overall, FLASH is a valuable tool for enhancing the quality of genome assemblies by extending short reads.