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.

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:

Performing a de novo assembly locally

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 de novo assembly locally so without using the external calculation engine.

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