BS-Seeker3: An Ultra-fast, Versatile Pipeline for Mapping Bisulfite-treated Reads.

Method to optimally select samples for validation and resequencing

Fast in-silico normalization algorithm for NGS data

myVCF: a web-based platform for target and exome mutations data management

ALAPY COMPRESSOR: FASTQ lossless compressor

A tool to extract mappable reads from various library preparation protocols.

Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ratio calculations

Tools for analyzing NGS sequence data and aligned protein sequences

Polymorphic Edge Detection - An efficient polymorphism detector for NGS data

useful bash one-liners and scripts

CLAP - A pipeline used to process CLIP-seq (specifically PAR-CLIP, HITS-CLIP and iCLIP) data.

WOLAND is a multiplatform tool to analyze point mutation patterns using resequencing data from any organism or cell. It is implemented as a Perl and R tool using as inputs filtered unannotated or annotated SNV lists, combined with its correspondent genome sequences.

A collection of various tools useful for the deep analysis of data generated via the CRSSANT/rna2d3d pipeline.

pyAmpli: an amplicon-based variant filter pipeline for targeted enriched resequencing data

This project includes simulated and 'golden standard' datasets, software and scripts that we used to benchmark error correction tools

Miscellaneous tools for the analysis of NGS data

Extract unmapped read fragments from a sequence alignment map by evaluating it's concise idiosyncratic gapped alignment reports (CIGARs)

SRSF shape analysis framework for sequencing data

(Archived) This page is a record of my first formal NGS Project for Dr. Matesic of University of South Carolina (USC).

Program extracts a valuable information from an output vecscreen file