NGSReadsTreatment – A Cuckoo Filter-based Tool for Removing Duplicate Reads in NGS Data

RNA-CODE: A Noncoding RNA Classification Tool for Short Reads in NGS Data Lacking Reference Genomes

The number of transcriptomic sequencing projects of various non-model organisms is still accumulating rapidly. As non-coding RNAs (ncRNAs) are highly abundant in living organism and play important roles in many biological processes, identifying fragmentary members of ncRNAs in small RNA-seq data is an important step in post-NGS analysis. However, the state-of-the-art ncRNA search tools are not ...

Filtering duplicate reads from 454 pyrosequencing data

MOTIVATION Throughout the recent years, 454 pyrosequencing has emerged as an efficient alternative to traditional Sanger sequencing and is widely used in both de novo whole-genome sequencing and metagenomics. Especially the latter application is extremely sensitive to sequencing errors and artificially duplicated reads. Both are common in 454 pyrosequencing and can create a strong bias in the e...

Statistical Significance for NGS Reads Similarities

In this work we present a significance curve to segregate random alignments from true matches in by identity sequence comparison, especially suitable for sequencing data produced by NGS-technologies. The experimental approach reproduces the random local ungapped similarities distribution by score and length from which it is possible to asses the statistical significance of any particular ungapp...

ngsCAT Capture Assessment Tool for NGS data

A Cuckoo Filter Modification Inspired by Bloom Filter

Probabilistic data structures are so popular in membership queries, network applications, and so on. Bloom Filter and Cuckoo Filter are two popular space efficient models that incorporate in set membership checking part of many important protocols. They are compact representation of data that use hash functions to randomize a set of items. Being able to store more elements while keeping a reaso...