Privatre:bioinfomatics: Difference between revisions
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(Created page with "{| class="wikitable" |+ !Libraries !Description !References |- |Samtools |SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments | * https://samtools.sourceforge.net/ * https://sourceforge.net/projects/samtools/files/samtools/ * https://github.com/samtools/samtools/blob/develop/INSTALL |- | | | |- | | | |} == References == <references />") |
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* https://github.com/samtools/samtools/blob/develop/INSTALL | * https://github.com/samtools/samtools/blob/develop/INSTALL | ||
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|Breakdancer | |||
|BreakDancer uses CMake which is a cross-platform build tool. Basically it will generate a Makefile so you can use <code>make</code>. The requirements are the zlib, development [[library]], gcc, gmake, cmake 2.8+. Beginning with version 1.4.4, BreakDancer includes samtools as part of the build process | |||
<code># --recursive option is important so that it gets the submodules too | |||
$ git clone --recursive <nowiki>https://github.com/genome/breakdancer.git</nowiki></code> | |||
| | | | ||
* https://github.com/genome/breakdancer/tree/master | |||
* https://breakdancer.sourceforge.net/<nowiki/>https://vcru.wisc.edu/simonlab/bioinformatics/programs/install/breakdancer.htm | |||
* https://github.com/shendurelab/LACHESIS/issues/30 | |||
|- | |- | ||
|BWA | |||
|BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. | |||
| | | | ||
* https://bio-bwa.sourceforge.net/ | |||
* https://wikis.utexas.edu/display/bioiteam/BWA | |||
|} | |} | ||
== References == | == References == | ||
<references /> | <references /> | ||
Revision as of 11:37, 19 November 2023
| Libraries | Description | References |
|---|---|---|
| Samtools | SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments | |
| Breakdancer | BreakDancer uses CMake which is a cross-platform build tool. Basically it will generate a Makefile so you can use make. The requirements are the zlib, development library, gcc, gmake, cmake 2.8+. Beginning with version 1.4.4, BreakDancer includes samtools as part of the build process
|
|
| BWA | BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. |