I am working with a program that generates artificial FASTQ files from a given reference genome and it allows for read length customization. I am trying to produce several FASTQ files with different read lengths. Hence, I want to know what read lengths are produced by real sequencers such as those from Illumina. I found [this][1] site which states the maximum read length of some sequencers.

However, when stating, for example, that the maximum read length is 2 x 150 bp, is that supposed to mean that each end of a contig will be 150 bp long? Also, if that is the case, does this mean that the sequencer could be set up to produce read lengths equal to any number of base pairs less than 150? i.e. could the sequencer produce read lengths of 2 x 1 bp, 2 x 2 bp, 2 x 3 bp,...., 2 x 148 bp, 2 x 149 bp? Lastly, which one of those sequencers is the most commonly used for genomes which are about as long as, say, that of E. Coli?

 [1]: http://www.illumina.com/systems/sequencing.ilmn
*However, when stating, for example, that the maximum read length is 2 x 150 bp, is that supposed to mean that each end of a contig will be 150 bp long?*

No. Contigs are [something else][1] based on an assembled consensus sequence.

2 x 150 bp means that you have two 150 bp reads of sequence data from a single piece of DNA. The pair of reads are separated by an unspecified length based on the insert size (usually 200 to 1200 bp) which is size-selected during the sequencing prep. This picture might make things more clear.

<a href="http://commons.wikimedia.org/wiki/File:Mapping_Reads.png#mediaviewer/File:Mapping_Reads.png"><img alt="Mapping Reads.png" src="http://upload.wikimedia.org/wikipedia/commons/2/2e/Mapping_Reads.png" style="height:290px; width:402px" /></a>

[Mapping Reads][2] by [Suspencewl][3] - Own work. Licensed under [CC0][4] via [Wikimedia Commons][5].

The blown up read is 2 x 35. The insert size (bp between the sequencing adapters) is 400-500 bp. All of the reads in the picture could be used to assemble a single contig based on the consensus sequence.

For illumina sequencing, the read length is specified by the reagent kit, so you have limited flexibility there.

The MiSeq is capable of 15 Gb of sequence output. The *E. coli* genome is ~4.6 Mb in length so in a single run a MiSeq could easily sequence an *E. coli* genome at ultra-high depth.

 [1]: http://genome.jgi-psf.org/help/scaffolds.html
 [2]: http://commons.wikimedia.org/wiki/File:Mapping_Reads.png#mediaviewer/File:Mapping_Reads.png
 [3]: http://commons.wikimedia.org/wiki/User:Suspencewl
 [4]: http://creativecommons.org/publicdomain/zero/1.0/deed.en
 [5]: http://commons.wikimedia.org/wiki/