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Bioinformatics

Courses

Genome variant interpretation

Datasets

  • http://hgdownload.cse.ucsc.edu/goldenpath/hg19/chromosomes/
  • wget -c -O NA12878_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR194/ERR194147/ERR194147_1.fastq.gz
  • wget -c -O NA12878_2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR194/ERR194147/ERR194147_2.fastq.gz

Tools

Variant interpretation

  • bcbio-nextgen
  • GEMINI - GEMINI: a flexible framework for exploring genome variation.
  • snpEff - Genomic variant annotations and functional effect prediction toolbox.

Structure

Pairwise alignment

  • TODO: fill this section.

Multiple sequence alignment

  • MAFFT ★ - Best tool at the moment. Has a liberal license. Supports multiprocessing. Shows state-of-the-art accuracy.
  • MUSCLE - Maybe about as accurate as MAFFT, but does not support multithreading?
  • Clustal Omega - Reasonable performance and a good choice for making very large alignments.

Sources: