Privatre:bioinfomatics

Bioinfomatics

A combined technologies with biology, computer science, mathmatics and statistics.

Bioinfomatics workflow steps

1. quality control assessmemt steps
2. sequence alignment
3. data summarization into genes/regions
4. data annotation to genomics features
5. statistical comparisons
6. mutltiomic ingetration

We can use BIOConda

Bioconda only supports python 2.7, 3.6, 3.7, 3.8 and 3.9 -> DLS38 can be used

Source compile Method

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
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 # --recursive option is important so that it gets the submodules too $ git clone --recursive https://github.com/genome/breakdancer.git	https://github.com/genome/breakdancer/tree/master https://breakdancer.sourceforge.net/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