HiLive Code
Realtime Alignment of Illumina Reads - old repo
Status: Beta
Brought to you by:
lindnerm
File | Date | Author | Commit |
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lib | 2015-09-26 |
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[41c5c3] Removed unnecessary CMakeLists file |
tools | 2015-09-20 |
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[726e92] Added README; optimized CMakeLists.txt; set def... |
CMakeLists.txt | 2015-09-20 |
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[726e92] Added README; optimized CMakeLists.txt; set def... |
LICENSE | 2015-09-16 |
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[34e6ce] Initial commit |
README | 2015-09-20 |
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[726e92] Added README; optimized CMakeLists.txt; set def... |
HiLive - Live Mapping of Illumina reads 1. Description -------------- HiLive is a read mapping tool that maps Illumina HiSeq (or comparable) reads right in the moment when they are produced. This means, read mapping is finished as soon as the sequencer is finished. 2. Website ---------- The HiLive project website is https://sourceforge.net/projects/hilive/ There you can find the latest version of HiLive, source code, documentation, and examples. 3. Installation --------------- If the binary distribution from the project website does not work for you, you can still compile HiLive from source. Make sure that the following dependences are installed: - cmake (>= 2.8) - boost (system, filesystem, program_options) - zlib - lz4 Check out the source code from the project website. Compile HiLive with: cd [hilive-code] mkdir build && cd build cmake .. make To compile HiLive with a different k-mer size than k=15 make the following adjustment (here: k=10): cmake -DHiLive_K 10 .. make 4. Usage -------- HiLive has two components: - hilive-build: build the k-mer index of the reference genome - hilive: the read mapper itself Using hilive-build: Building a k-mer index from FASTA file input.fa: hilive-build input.fa The index is written to input.fa.kix Building an index from a large reference genome. Here is makes sense to use trimming, i.e. removing k-mers from the index that occurr more than 1000 times (for example) in the index. The index is written into the file trimmed.kix hilive-build -t 1000 -o trimmed.kix input.fa Using hilive: To map reads in a 100bp run using default settings: hilive /path/to/BaseCalls /path/to/index.kix 100 We recommend to adjust the numbers of threads used by HiLive with -n. If possible, make use of all threads on the machine! Please consult the project website for more details on the parameters! 5. License ---------- See the file LICENSE for licensing information. 6. Contact ---------- Please consult the HiLive project website for questions! If this does not help, please feel free to consult: Martin S. Lindner <martin (at) mail-lindner.de> (technical contact) Bernhard Y. Renard <renardb (at) rki.de> (project head)