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).




Usage on Bridges


To see what versions of FLASh are available type

module avail flash

To see what other modules are needed, what commands are available and how to get additional help type

module help  flash

To use FLASh, include a command like this in your batch script or interactive session to load the FLASh module:

module load flash

Be sure you also load any other modules needed, as listed by the module help flash command.


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