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Absolve

Absolve is a command line tool for annotating antibody variable domain sequences with

*  ORF
*  Framework and CDR regions
*  Kabat Numbering
*  Germline Assignment
*  Somatic Hypermutation 

Absolve accepts fasta files as input, or fastq files as either single or paired-end reads. It generates results for the input sequences as either a single tab-delimited file or multiple tab-delimited files if requested. Germline sequences are provided for human, but users maybe provide their own fasta formatted database files that have been indexed by BWA.

Absolve is written in C++ and links directly to BWA and HMMR libraries included.

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Documentation

Please examine the manual for more detailed documentation of program parameters and design

./docs/manual/Absolve.html

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Build the application

Supported platforms: * Linux * Mac OSX

1. Platform/OS dependencies:

   • C++11 compatible compiler
   • C mathematical library. (libm)
   • Compression library. (libz)
   • POSIX multithreading library. (libpthread)
   • Specific Boost libraries: boost_system, boost_filesystem, boost_iostreams, boost_regex
   • CMake Ver 3.5 or greater

2. Build the included dependencies. Copies of BWA and HMMR are included.

	cd dep/
	tar -zxvf bwa-0.7.12.tar.gz
	tar -zxvf hmmer-3.1b2.tar.gz
	cd bwa-0.7.12/ 
	make
	cd ..
	cd hmmer-3.1b2/
	./configure
	make 
	cd ../..

3. Configure environment

		source ./SETUP.bash `pwd`

4. Build release version

		cmake CMakeLists.txt
		make clean
		make

5. Make sure all tests run ok

		cd test
		cp -R testrun.ref.template testrun.ref
		./RunTest.bash
		cd ..

6. Invoke "absolve.bash" to run

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