claymcleod / genomics-primer Goto Github PK

This repository contains all of the resources I have found helpful in studying genomics from the ground up.

1. A Brief Guide to Genomics by the National Human Genome Research Institute
2. Overview of genomic file formats. Introduction to common file types for genomics.
3. FastQ file specification. Illumina raw data format specification. In general, this is thought to be the industry standard.
4. SAM/BAM file specification. This is the industry standard file-type for aligned sequence data. Know this format like the back of your hand.

• Samtools: manipulate and perform common tasks for SAM/BAM/CRAM files.
• BWA aligner: Industry standard WGS/WXS aligner
• STAR aligner: Industry standard Transcriptome aligner
• Picard: Swiss-army knife of genomics
• GATK: Genome Analysis Toolkit, industry standard variant caller.
• FastQC: Industry standard raw data quality check software.
• htseq: Useful for counting gene expression

• 1000 genomes: The "thousand genome project" is a well-known project that houses raw/variant data from 1000 people across the world.
• dbGaP: NIH (U.S. based) genomics repository
• EGA: EBI (European based) genotype-phenotype repository

• dbSNP: de-facto single nucleotide polymorphism database. Mostly research oriented.
• OMIM: The "Online Mendelian Inheritance in Man" is a catalog that maps genotypes -> phenotypes. A great resource for handcrafting articles and literature curation.

• ClinVar: clinical significance of variations for humans.
• PolyPhen-2: The "Polymorphism Phenotyping v2" tool attempts to predict the functional/structural effects of a variant on a human protein.
• SIFT: The SIFT tool attempts to predict whether an amino acid substitution affects protein function.
• FATHMM: FATHMM stands for "functional analysis though hidden markov models". This tool attempts to predict the functional affect of a variant on the resulting protein.

• Machine Learning in Genomic Medicine
• Machine Learning Applications in Genetics and Genomics