Sequence read sets

A sequence read set is designed to hold large sets of short reads generated by next generation sequencing (NGS). Base sequences and their associated quality scores are stored for single-end and paired-end reads, originating from various high-throughput pyrosequencing platforms such as Roche 454, Illumina Solexa, Ion Torrent, etc.

Importing FASTQ files and FASTQ file links

Essentially, there are two ways to import FASTQ files in your BioNumerics database: the default import method stores the sequence reads in the BioNumerics database and the second import method only imports the links to the location of the FASTQ files. In this tutorial both options are described.

Hotfix for CE Store Uploader issue

Recently, when I post jobs on the Applied Maths cloud Calculation Engine for which the fastq.gz files are stored on a local file server, the job statuses often remain "WaitingQueued" for more than 24 hours after which the jobs fail. I haven't experienced this before, what could be the reason?

Hotfix for importing sequence read sets from NCBI

During import of a sequence read set as link via its NCBI SRA accession number, I get following error message: Some accession codes could not be found on NCBI (SRA): <SraAccession>: ||||||||400|Unsupported protocol

Performing a de novo assembly on the external calculation engine

This tutorial illustrates how to import FASTQ file links into a BioNumerics database and finally how to perform a de novo assembly on the external calculation engine.

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