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Forum: Bioinformatics 11-04-2016, 09:38 AM
Replies: 3
Views: 2,001
Posted By akorobeynikov
Yes, this is known problem on Sierra. We're...

Yes, this is known problem on Sierra. We're working on the fix. Stay tuned!
Forum: De novo discovery 12-03-2015, 03:09 AM
Replies: 5
Views: 3,222
Posted By akorobeynikov
Since you're having multiple copies of 16s then...

Since you're having multiple copies of 16s then you need to have sufficiently long insert length to allow assembler resolve this repetitive region. Otherwise, indeed, everything will be inside single...
Forum: Bioinformatics 12-03-2015, 02:33 AM
Replies: 7
Views: 3,752
Posted By akorobeynikov
This is certainly not true. I'd suggest...

This is certainly not true.


I'd suggest to give SPAdes a try. If uncertain - just contact SPAdes support for some advices.
Forum: Bioinformatics 03-27-2015, 05:32 AM
Replies: 4
Views: 6,623
Posted By akorobeynikov
Check this...

Check this http://seqanswers.com/forums/showthread.php?t=1529 for k-mer coverage. Use k=55 for SPAdes in this case.
Forum: Bioinformatics 03-27-2015, 05:24 AM
Replies: 4
Views: 6,623
Posted By akorobeynikov
Yes, like in Velvet, this is the average k-mer...

Yes, like in Velvet, this is the average k-mer coverage of a contig/scaffold. Use the last k-mer length if you need to convert to read coverage.
Forum: Pacific Biosciences 01-11-2015, 11:59 AM
Replies: 11
Views: 2,759
Posted By akorobeynikov
SPAdes cannot be used for de novo assembly of...

SPAdes cannot be used for de novo assembly of PacBio reads alone (unless you have pre-corrected or CCS reads). As stated in the manual, SPAdes performs *hybrid* assembly of your Illumina / IonTorrent...
Forum: Illumina/Solexa 12-08-2014, 10:45 AM
Replies: 35
Views: 14,770
Posted By akorobeynikov
This is more or less expected. IonHammer is...

This is more or less expected. IonHammer is conservative - when it fails to correct something it preserves the original read and postpones the final decision to assembler. In general we suggest not...
Forum: Illumina/Solexa 12-02-2014, 11:04 PM
Replies: 35
Views: 14,770
Posted By akorobeynikov
The second variant looks correct to me, basically...

The second variant looks correct to me, basically you need to specify the first and the second read of a fragment and how they were read (in which direction).

Anyway, you can simply feed the data...
Forum: Illumina/Solexa 12-01-2014, 10:44 PM
Replies: 35
Views: 14,770
Posted By akorobeynikov
You need to split them before, yes. Make sure you...

You need to split them before, yes. Make sure you specified the correct library type (mate pairs) and the correct orientation (whatever you have, e.g. even ff is supported). See...
Forum: Illumina/Solexa 12-01-2014, 09:59 AM
Replies: 35
Views: 14,770
Posted By akorobeynikov
You're missing the 5th possibility which is...

You're missing the 5th possibility which is actually the proper choice here. Basically:

1. Correct your Illumina reads using --only-error-correction mode
2. Correct your 454 reads using...
Forum: Pacific Biosciences 08-29-2014, 08:08 AM
Replies: 3
Views: 1,599
Posted By akorobeynikov
You may want to give SPAdes a try in its hybrid...

You may want to give SPAdes a try in its hybrid mode assembling Illumina + PacBio reads instead of Cerulean. You can also feed SPAdes your current contigs as 'trusted contigs'.
Forum: Bioinformatics 08-10-2014, 02:07 AM
Replies: 1
Views: 1,825
Posted By akorobeynikov
Correct. If there are multiple possible positions...

Correct. If there are multiple possible positions where the read can be aligned to, then the aligners often emit only one random alignment. Therefore in the repetitive regions you may see such SNPs,...
Forum: Pacific Biosciences 08-10-2014, 01:59 AM
Replies: 20
Views: 5,410
Posted By akorobeynikov
You may try to use SPAdes for hybrid Illumina +...

You may try to use SPAdes for hybrid Illumina + PacBio assembly. It will happily use your PacBio data both for filling in unrepresented parts in your Illumina data and resolve repeats.
Forum: Illumina/Solexa 05-23-2014, 11:17 AM
Replies: 35
Views: 14,770
Posted By akorobeynikov
SPAdes uses PacBio reads for repeat resolution....

SPAdes uses PacBio reads for repeat resolution. So, it uses original uncorrected reads.




Usually such warnings indicate that you have quite uneven coverage and trying to assemble in...
Forum: Illumina/Solexa 05-19-2014, 01:23 PM
Replies: 35
Views: 14,770
Posted By akorobeynikov
The reported coverages are the average k-mer...

The reported coverages are the average k-mer coverage of the contig. Use the last k-mer iteration for the value of a k-mer length.
Forum: Illumina/Solexa 04-16-2014, 02:08 AM
Replies: 35
Views: 14,770
Posted By akorobeynikov
This may be non-trivial. But probably yes - try...

This may be non-trivial. But probably yes - try to provide them as "sanger" reads.

You may also want to pre-correct them as IonTorrent reads (--iontorrent --only-error-correction), and try to...
Forum: Illumina/Solexa 04-16-2014, 02:06 AM
Replies: 35
Views: 14,770
Posted By akorobeynikov
Right. Basically, filtered subreads are the...

Right. Basically, filtered subreads are the result of "P_Filter" step which can be performed at SMRT portal (and usually filtered subreads is what one would obtain from 3rd party sequencing provider).
Forum: Illumina/Solexa 04-02-2014, 12:07 PM
Replies: 35
Views: 14,770
Posted By akorobeynikov
I looked over manual and found nothing which may...

I looked over manual and found nothing which may indicate so. The manual clearly states that "consensus_contigs.fasta - file in FASTA format with a set of constructed consensus contigs".


It...
Forum: Illumina/Solexa 03-31-2014, 11:51 PM
Replies: 35
Views: 14,770
Posted By akorobeynikov
Yes, DipSPAdes can use PacBio reads. Currently it...

Yes, DipSPAdes can use PacBio reads. Currently it uses them only for haplocontigs construction, so this may be a bit suboptimal.

Also, I would suggest you to disable --careful option for initial...
Forum: Illumina/Solexa 03-31-2014, 02:54 AM
Replies: 35
Views: 14,770
Posted By akorobeynikov
I would suggest reading DipSPAdes manual...

I would suggest reading DipSPAdes manual (http://spades.bioinf.spbau.ru/release3.0.0/dipspades_manual.html) in order to understand the differences between SPAdes and DipSPAdes output.

In short:...
Forum: Illumina/Solexa 03-03-2014, 10:22 PM
Replies: 6
Views: 2,322
Posted By akorobeynikov
Another thing to consider: if you will want to...

Another thing to consider: if you will want to assemble your data de novo instead of mapping, then you will need to use an assembler which can cope with huge variations of coverage and MDA-induced...
Forum: Illumina/Solexa 03-03-2014, 10:02 AM
Replies: 35
Views: 14,770
Posted By akorobeynikov
You can definitely give SPAdes a try. The...

You can definitely give SPAdes a try. The instructions to assemble 2x250 reads can be found in the manual (http://spades.bioinf.spbau.ru/release3.0.0/manual.html#sec3.4), though everything described...
Forum: Ion Torrent 01-28-2014, 01:08 PM
Replies: 7
Views: 3,629
Posted By akorobeynikov
Well, I never did this by myself, but rumors are...

Well, I never did this by myself, but rumors are that you still
may try to assemble them in single-cell mode. I'd select the standard set of kmers, that is - 21,33,55
Forum: Ion Torrent 01-28-2014, 11:02 AM
Replies: 7
Views: 3,629
Posted By akorobeynikov
You may also consider SPAdes 3.0, which contains...

You may also consider SPAdes 3.0, which contains experimental IonTorrent error correction and assembly module.
Forum: Pacific Biosciences 01-28-2014, 10:52 AM
Replies: 9
Views: 4,107
Posted By akorobeynikov
SPAdes 3.0 (http://bioinf.spbau.ru/en/spades)...

SPAdes 3.0 (http://bioinf.spbau.ru/en/spades) includes support for hybrid assemblies from Illumina/IonTorrent+PacBio. Additional information (like old contigs, Sanger reads) can be added as well.
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