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.

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.

FASTQ files

This data set contains 10 gzipped fastq files of 5 paired end read data file pairs coming from Staphylococcus aureus and an Excel file containing some metadata on the sequence read sets. This data was generated by Illumina MiSeq whole genome sequencing and downloaded from NCBI.

Performing a resequencing assembly

This tutorial illustrates how to import FASTQ files into a BioNumerics database, how to obtain a quick overview of the basic statistics on read quality and read length, and finally how to perform a resequencing assembly against a reference sequence.

Velvet k-mer length

I have a problem with de novo assembly of my sequence reads. The problem manifests itself in different ways:

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