Tag Archives: bioinformatics

Primer Trimming Challenge

In DNA sequencing, we add primers and adapters to the ends of sequences. These are short (typically <50bp) known sequences, that we use so we can identify different kinds of sequences. You can find out more about the adapters in this YouTube video.

This challenge is to write software to efficiently detect and remove the primers and adapters from a fastq format file.

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ReadMapper: a program that maps sequencing reads to a nucleotide backbone, and creates a publication quality figure.


ReadMapper is based on R code that was written to analyze our inhouse data.  The code has been modified to make it user friendly and allow other people, who are not as versed in the R language, to be able to map sequencing reads to a nucleotide backbone, and create publication quality figures.  In our project we were mapping translatome data to the genome of the phage Lambda (this is what the included sample data is), as well as the currently annotated gene open reading frames.  Which looks just like the figure below.

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