Software for second-generation sequencing data analysis

This software is under heavy development. Please email with any comments or questions.

 

Srfim

Short-Read Filtering and Intensity-Modeling. This package does model-based quality assessment and base-calling for Illumina GA data.
[download] [usage]

 

SRAdata

Read Illumina intensity and sequence data from downloaded from NCBI's Short Read Archive.
[download] [usage]

 

metagenomeSeq

Statistical analysis of sparse high-throughput sequencing data.
Available in Bioconductor

 

BlindCall

Ultra-fast base-calling of second-generation sequencing data by blind deconvolution.
[download] [data]

 

SERVIC4E

Effective detection of rare variants in pooled DNA samples. This is joint work with Tejasvi Niranjan at the Johns Hopkins Institute of Genomic Medicine.
[download]

 

Rsolid

Preprocessing for color-calling of ABI SOLiD data.
[download and usage]

Contact :

hcorrada@umiacs.umd.edu

 

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