Code

Major  Programs 

Major software supported by the Bailey lab

See our github at https://github.com/bailey-lab



SeekDeep

Single base de novo resolution of deep sequenced PCR amplicons.  Accurate down to 0.2% abundance in most instances for complex mixtures. Also, provides improved standard OTU analyses a defined percent similarity.

Citation: Hathaway  et al. SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing. Nucleic Acids Res. 2018 Feb 28;46(4):e21

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.

PathWeaver  

Improved local assembly optimized to generate haplotypes in polyclonal mixtures. 
Currently in alpha testing.

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.
See the CnvDetectD2  web page


Other code

Specialized code and in house scripts from various projects and publications. 


MinorAlleleCatcher

The code filters reads to accurately identify alternative SNP frequencies in pooled DNA sequencing libraries. We recommend using a newer implementation of this code.  See minorallelecatcher page for more info. This was used in Taylor et al  JID 2015

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.
See the CnvDetectD2  web page.

Older Code

This code is no longer being actively developed but we still find it useful and so do others.

parasight

Old software that still provides useful interactive visualization software. Developed by Jeff during his PhD for visualizing segmental duplications within mammalian genomes, it is still used in the lab to rapidly visualize and interact with data. See. baileylab.brown.edu/parasight. Someday we might revamp this program and move it out of Perl/Tk.