SeekDeep

Version 3.0.1

Bioinformatic Tools for analyzing targeted amplicon sequencing developed by the UMASS Med Bailey Lab

Checkout the website bellow for more details
http://seekdeep.brown.edu/

Please cite the following citation: Hathaway, Nicholas J., Christian M. Parobek, Jonathan J. Juliano, and Jeffrey A. Bailey. 2017. “SeekDeep: Single-Base Resolution de Novo Clustering for Amplicon Deep Sequencing.” Nucleic Acids Research, November. https://doi.org/10.1093/nar/gkx1201.

Installing

See installing tab on http://seekdeep.brown.edu/ for full details for installing for each operating system.

Dependecnies

Need to have at least g++-7, or clang++-3.8 compiler, the default assumption is g++-7, can change what compilier is used by giving -CC and -CXX to ./congifure.py
Examples

For g++-7

./configure.py -CC gcc-7 -CXX g++-7

For clang
For Mac OsX make sure clang version is 7.0 or greater

./configure.py -CC clang -CXX clang++  

Also though SeekDeep does not use cmake, several of the libraries it uses do depend on cmake so it needs to be present.

To Install latest version (defaults to g++-7 or defaults to clang on Mac)

git clone https://github.com/bailey-lab/SeekDeep.git   
cd SeekDeep  
git checkout master
./configure.py  
./setup.py --compfile compfile.mk --outMakefile makefile-common.mk
make   

Bash Completion

SeekDeep tends to have long flags so that they can be clear what they do but it's somewhat annoying to type them out so bash completion has been added. Put the content of the file at bashCompletion/SeekDeep into a file ~/.bash_completion and it will be source on your next login or use the bellow command while in the SeekDeep directory

./setup.py --addBashCompletion  

Which will actually do exactly described above, afterwards while typing flags use the tab key to complete them

Tutorials

Tutorials and detailed usages located at http://seekdeep.brown.edu or email nicholas.hathaway@umassmed.edu for more information