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.
Please examine the manual for more detailed documentation of program parameters and design
Supported platforms: * Linux * Mac OSX
-
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
-
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 ../..
- Configure environment
source ./SETUP.bash `pwd`
- Build release version
cmake CMakeLists.txt
make clean
make
- Make sure all tests run ok
cd test
cp -R testrun.ref.template testrun.ref
./RunTest.bash
cd ..
- Invoke "absolve.bash" to run
eof