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 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

Importing FASTQ files and linked database entry information

This tutorial illustrates how to import run information from an Excel file, and how to import and link fastq files to these entries. This tutorial also illustrates how to obtain a quick overview of the basic statistics on read quality and read length, and how predefined charts are used to get a more indetailed view on these characteristics.

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.

Importing FASTQ files and 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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