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Proceeds by simultaneously considering both ends of paired reads generating elongated reads. ELOPER is a pre-processing tool for pair-end sequences that produces a better read library for assembly programs. It theoretically doubles read-lengths while halving the number of reads. This method exploits the notion that the paired-end information essentially doubles the read length, permitting the detection of up to double the original overlap while maintaining the minimum required sequence overlap. ELOPER thus provides a valuable pre-processing for improved de novo assemblies of short paired-end libraries.
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Uses as a splice-aware aligner for short and long reads. BBMap is shown to be a fast and accurate aligner, capable of correctly handling an overall wider variety of references, reads, and mutations than others. It has particularly outstanding performance with deletions, especially long ones, that other aligners cannot handle at all. It can output many different statistics files, such as an empirical read quality histogram, insert-size distribution, and genome coverage, with or without generating a sam file.
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