Category: "Bioinformatics"

BCL files

December 30th, 2016
As part of the Primary Analysis Illumina sequencing machines measure the intensity of the channels used for encoding the different bases and identify the most likely base at a given position of a sequencing read (tag). The Real Time Analysis (RTA)… more »

CRAM format

January 7th, 2015
CRAM files are compressed versions of BAM files containing (aligned) sequencing reads. They represent further file size reduction for this type of data that is generated at ever increasing quantities. more »

NGS reads and their Scores

August 1st, 2014
Generating mapping quality scores For each alignment, BWA calculates a mapping quality score, which is the Phred-scaled probability of the alignment being incorrect. The algorithm is similar to MAQ's except that in BWA we assume the true hit can alwa… more »

Testing for Equivalence

August 1st, 2014
To assess whether a new test (e.g. a medical device testing for disease or non-disease status) is equivalent to an existing test, the following measures can be reported. If the existing test is not perfect, the FDA recommends to report the positive… more »

SNP calling & the VCF format

May 16th, 2014
SNP calling refers to the process of identifying posititions where the genome of a sequenced sample differs to that of the reference genome. This might lead to finding disease-causing genomic alterations. In the following I wanted to re-align short NGS… more »