Hiseq Analysis Software Alignment

Question

[Nicola Casiraghi]

Dear all, I want to test the new Isaac aligner by Illumina. Thus, I have downloaded and installed the HiSeq Analysis Software (stable version of Isaac) from Illumina website. Now I am trying to perform a comparison between BWA aligner and Isaac giving as input the same FASTQ file (paired-end reads). Looking at the HiSeq manual page 27, most of the required inputs are "Sequencing Run Files" generated from Illumina's sequencing software. The problem is that I do not have this kind of information for my starting fastq files. Is it possible to run Isaac without these files using as input the fastq file? In other words, can I use Isaac as a general aligner or it can be used only with Illumina generated data?

Thank you for the help

Answer 1

[Istvan Albert]

It appears that this tool operates on instrument produced output files (*.bcl) which seems to be a very unusual requirement.

Only the Illumina instruments produce these files and we usually convert as soon as possibly to FastQ formats. In addition the tool seems to require a number of run specific configuration files such as a sample sheet and Runinfo.xml that again used to be relevant only very early in the conversion process. For that reason these are never distributed.

It seems that this software is meant to facilitate the common use cases so that these can be run directly after a sequencing run is complete.

[DG]

Probably the closest you can get (without asking for these files, if they even still have them, from the sequencing provider) would be to run the open-source version of isaac available on GitHub. I don't think it is identical, there are some differences, but it would probably give you an idea of how it compares to bwa anyway.

[Matt Shirley]

Link? I can't find the repository you mention.

[DG]

https://github.com/sequencing/isaac_aligner

[Nicola Casiraghi]

Many thanks to everybody for clear replies and suggestions. Dear Dan Gaston, do you have any experiences with Isaac_aligner? I failed several times trying to install it.

[DG]

Unfortunately I don't. I knew about the repo because I had some plans, like you, on testing it compared to bwa and a few other aligners. But I didn't get around to trying to actually built it from the source.