Code
Major Programs
Major software supported by the Bailey lab
See our github at https://github.com/bailey-lab
See our github at https://github.com/bailey-lab
SeekDeep![]() Citation: Hathaway et al. SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing. Nucleic Acids Res. 2018 Feb 28;46(4):e21
For more info see:
baileylab.brown.edu/SeekDeep |
MIP Wrangler
Software for rapid analysis of molecular inversion probes in numerous samples. It is currently alpha software being tested by ourselves and our collaborators.
Currently in alpha testing.
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PathWeaver
Improved local assembly optimized to generate haplotypes in polyclonal mixtures.
Currently in alpha testing.
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CnvDetectD2
CNV detection optimized for Plasmodium whole genome sequencing. D2 is for Depth and Discordancy of reads--the two main metrics leveraged in the program. Together they provide for more accurate detection across the entire core genome.
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Other code
Specialized code and in house scripts from various projects and publications.MinorAlleleCatcher
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Whole genome
CNV detection optimized for Plasmodium whole genome sequencing. D2 is for Depth and Discordancy of reads--the two main metrics leveraged in the program. Together they provide for more accurate detection across the entire core genome.
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Older Code
This code is no longer being actively developed but we still find it useful and so do others.