https://github.com/genentech/absolve
Absolve antibody variable domain sequence analysis
https://github.com/genentech/absolve
Last synced: about 1 year ago
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Absolve antibody variable domain sequence analysis
- Host: GitHub
- URL: https://github.com/genentech/absolve
- Owner: Genentech
- License: mit
- Created: 2018-09-12T22:18:02.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2018-09-13T22:39:17.000Z (over 7 years ago)
- Last Synced: 2023-10-26T05:44:02.551Z (over 2 years ago)
- Language: C++
- Homepage:
- Size: 6.05 MB
- Stars: 14
- Watchers: 15
- Forks: 8
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: COPYING
Awesome Lists containing this project
README
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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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