Question: Illumina Instrument Type from fastq?
3
gravatar for andrew.j.skelton73
20 months ago by
Newcastle Upon Tyne
andrew.j.skelton734.2k wrote:

Hi,

Any idea if there's a way to get the Instrument type (i.e. NextSeq, HiSeq, etc), from the instrument name field in the Fastq read header? - I've tried looking for a map of sorts in Illumina's documentation, but to no avail.

Thanks,

fastq • 2.7k views
ADD COMMENTlink modified 10 weeks ago by Devon Ryan76k • written 20 months ago by andrew.j.skelton734.2k

Biostars.org is my one stop solution for bioinformatics info and analysis software Keep it up.

ADD REPLYlink written 20 months ago by mmulinge0
7
gravatar for genomax
20 months ago by
genomax42k
United States
genomax42k wrote:

There was a post @SeqAnswers where we had a recap of the types of sequencer specific fastq headers (my google-fu has not turned up that post yet). Following is a very rough approximation of start of fastq headers that are sequencer specific.

Edit: Just want to add that it is possible to change the default read header in one of the set up files (so the following may not always be true).

@HWI-Mxxxx or @Mxxxx - MiSeq
@HWUSI - GAIIx
@HWI-Dxxxx - HiSeq 2000/2500
@Kxxxx - HiSeq 3000(?)/4000
@Nxxxx - NextSeq 500/550

ADD COMMENTlink modified 20 months ago • written 20 months ago by genomax42k
1

Actually, the MiSeq read headers should be @Mxxxx

ADD REPLYlink written 20 months ago by igor5.2k
1

I don't know if those are still the default headers. Our new MiSeq outputs '@Mxxx' headers so, unless the FAS reconfigured it upon installation, it's the current default. Similarly, our HiSeq headers are not prefaced with '@HISEQ'.

The FCIDs are generated automatically during the flow cell scan, which is why I recommended using those to unambiguously distinguish the instruments. But I have not yet been able to find the complete code for conversion. I'll continue digging.

ADD REPLYlink written 20 months ago by harold.smith.tarheel4.0k
1

That is why I added a disclaimer.

It is possible to reconfigure the default headers (we have several HiSeq/MiSeq and the headers are slightly different). I have not looked through the config files to see where exactly this is set.

I remember that the FAS's have access to a special illumina tool/database where they can lookup kit/flowcell ID's but I don't think that tool is available to us.

ADD REPLYlink written 20 months ago by genomax42k
1

Do you mean FCID = Name of the data folder?

That generally has the format

For HiSeq

YYMMDD_InstrumentSerialNumber_RunNumber*_[A/B]FlowCellBarcode

For MiSeq

YYMMDD_InstrumentSerialNumber_RunNumber*_000000000-FlowCellBarcode

YYMMDD - Date the run started
*RunNumber - Cumulative run number (incremented by 1 for each run) on that sequencer.
A/B - signifies the flowcell position (in case of instruments that can run 2 FC at a time).

These names are configurable in a .cfg settings file and will give one an idea of the kind of sequencer it is (provided the default naming scheme is left intact).

ADD REPLYlink modified 20 months ago • written 20 months ago by genomax42k
1

FCID = flow cell identifier (same as your FlowCellBarcode). In the read identifier, it's the third field.

ADD REPLYlink written 20 months ago by harold.smith.tarheel4.0k

Yes! That's what I was looking for, and I vaguely remember seeing the same post on seq answers too! This post maybe?

ADD REPLYlink written 20 months ago by andrew.j.skelton734.2k
1

That is one of them. I seem to recollect that there was another one specifically like the question you asked.

ADD REPLYlink written 20 months ago by genomax42k

HiSeq 3000 starts with a J, not a K. Also, our HiSeq 2500 defaults to SNXXXXX.

Edit: Apparently HiSeq 3000s can start with either (consistency!). I bet our HiSeq 2500 starts with an S because it started life as a 2000 and got an upgrade.

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by Devon Ryan76k
6
gravatar for harold.smith.tarheel
20 months ago by
United States
harold.smith.tarheel4.0k wrote:

Illumina provided the following information regarding FCID mapping to instruments. The indicated characters are the last four of the nine-character FCID (excepting MiSeq). Please note that this is not comprehensive and there may be new additions in the future.

AAXX = Genome Analyzer
BCXX = HiSeq v1.5
ACXX = HiSeq High-Output v3
ANXX = HiSeq High-Output v4
ADXX = HiSeq RR v1
AMXX, BCXX =HiSeq RR v2
ALXX = HiSeqX
BGXX, AGXX = High-Output NextSeq
AFXX = Mid-Output NextSeq
5 letter/number = MiSeq

ADD COMMENTlink modified 20 months ago • written 20 months ago by harold.smith.tarheel4.0k

Thank you for getting this from Illumina.

While it does not conclusively associate a run with the kind of sequencer used (I think some of the HiSeq flowcells can be used on multiple models) it does provide useful information. Also the chances of flowcell ID being altered (except with SRA :-)) are small so this association should be more reliable.

ADD REPLYlink modified 20 months ago • written 20 months ago by genomax42k

What kind of instrument uses flowcells ending with BBXX? Here is the read sequence id line:

@ERR1417747.1 K00150:65:H77FVBBXX:7:1101:1570:1297 length=150
ADD REPLYlink modified 11 months ago • written 11 months ago by steven.davis10

The first part @ERR1417747 is SRA accession ID that get's tacked on (unless you use -F to regenerate sequence headers in the original Illumina format). Considering the sequencer ID K00150 that follows this should be a HiSeq 3000/4000 run.

ADD REPLYlink written 10 months ago by genomax42k

I got some fastq files, the id is like:

@FCH7HCYADXY:1:1101:10595:1825

what kind of instrument can it be? How can I get the latest RCID description?

ADD REPLYlink written 6 months ago by liangzebin556610
3
gravatar for Devon Ryan
10 weeks ago by
Devon Ryan76k
Freiburg, Germany
Devon Ryan76k wrote:

I realize that this is a year and a half late, but here is some code from 10X that incorporates both the flow cell ID and the machine ID to figure out the run type.

ADD COMMENTlink written 10 weeks ago by Devon Ryan76k

Fantastic find - really useful.

ADD REPLYlink written 10 weeks ago by andrew.j.skelton734.2k

I wonder if anyone has NovaSeq data so we could add that info here...

ADD REPLYlink written 10 weeks ago by Devon Ryan76k
2

Not 100% sure: S2 cells "H[A-Z,0-9]{4}DMXX$"
Sequencer serial may be "A[0-9]{6}$" for NovaSeq 6000.

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by genomax42k

Well that was quick (I notice now that 10X has a line for the NovaSeq in the source code I linked to).

ADD REPLYlink written 10 weeks ago by Devon Ryan76k

Guess that number is for S2 FC. So someone will have to give us data for S1/S4.

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by genomax42k
1

Still doing calibration runs on the nova at my institute, but I'll update when I get some data through

ADD REPLYlink written 10 weeks ago by andrew.j.skelton734.2k
1
gravatar for harold.smith.tarheel
20 months ago by
United States
harold.smith.tarheel4.0k wrote:

I believe you can extract the instrument type from the FCID in the read identifier (e.g. our HiSeq FCIDs all end in 'ACXX', MiSeqs all start with 'MS'), but you may need to contact Illumina to determine the complete code.

ADD COMMENTlink modified 20 months ago • written 20 months ago by harold.smith.tarheel4.0k
1

This was along the lines of what I was thinking, as there are similar tags in all the nextSeq data I see coming through, however I was hoping somebody had a handy map of these in some dark corner of the internet I've not come across yet!

ADD REPLYlink written 20 months ago by andrew.j.skelton734.2k
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