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

Bioinfomatics curated software list

• Package suites
• Data Tools
  • Downloading
  • Compressing
• Data Processing
  • Command Line Utilities
• Next Generation Sequencing
  • Workflow Managers
  • Pipelines
  • Sequence Processing
  • Data Analysis
  • Sequence Alignment
    • Pairwise
    • Multiple Sequence Alignment
    • Clustering
  • Quantification
  • Variant Calling
    • Structural variant callers
  • BAM File Utilities
  • VCF File Utilities
  • GFF BED File Utilities
  • Variant Simulation
  • Variant Prediction/Annotation
  • Python Modules
    • Data
    • Tools
  • Assembly
  • Annotation
• Long-read sequencing
  • Long-read Assembly
• Visualization
  • Genome Browsers / Gene Diagrams
  • Circos Related
• Database Access
• Resources
  • Becoming a Bioinformatician
  • Bioinformatics on GitHub
  • Sequencing
  • RNA-Seq
  • ChIP-Seq
  • YouTube Channels and Playlists
  • Blogs
  • Miscellaneous

• Online networking groups

File format in Bioinfomatics

This section explains some of the commonly used file formats in bioinformatics

File formats	File extensions
FASTA	.fa, .fasta, .fsa
FASTQ	.fastq, .sanfastq, .fq
SAM (Sequence Alignment Map)	file.sam
BAM	file.bam
VCF (Variant Calling Format/File)	file.vcf
GFF (General Feature Format or Gene Finding Format)	file.gff2, file. gff3, file.gff
GTF (Gene Transfer format)	file.gtf

Usufull Tutorial Link

• https://vcru.wisc.edu/simonlab/bioinformatics/programs/
• https://github.com/danielecook/Awesome-Bioinformatics
• https://mybiosoftware.com/
• https://bioinformatics.uconn.edu/resources-and-events/tutorials-2/
• Cluster system software modules - https://bioinformatics.uconn.edu/cbc_software/software-2/

We can use BIOConda

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

Lib and sources

Libraries	Description	References
rSeq: RNA-Seq Analyzer	https://jhui2014.github.io/rseq/	On 61 sever, /test/bioinfomatics/rseq/rseq-0.2.2-src
SNVMix2	https://github.com/shahcompbio/snvmix	imp@CGX-GPU:~/test/bioinfomatics/snvmix (master)$
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