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Forum: Bioinformatics 09-09-2015, 05:41 AM
Replies: 3
Views: 2,546
Posted By scalabrin
cutadapt has now this functionality

cutadapt has now this functionality
Forum: Bioinformatics 06-30-2015, 04:26 AM
Replies: 7
Views: 2,299
Posted By scalabrin
Try Denom,...

Try Denom, http://mus.well.ox.ac.uk/19genomes/IMR-DENOM/#DENOM

or mummer package with nucmer (but this is slow).
Forum: Bioinformatics 08-13-2014, 03:53 AM
Replies: 10
Views: 9,575
Posted By scalabrin
It depends on the assemblies you want to merge....

It depends on the assemblies you want to merge. If they are very similar to each other then there is no meaning to merge them. For example, if you run different assemblies with ABySS at different...
Forum: Pacific Biosciences 06-26-2014, 04:42 AM
Replies: 20
Views: 5,355
Posted By scalabrin
assembly merge

If you still need to do assembly merge, you can use GAM-NGS:

http://www.biomedcentral.com/1471-2105/14/S7/S6

Best,
Simone
Forum: Bioinformatics 07-27-2013, 11:04 AM
Replies: 10
Views: 9,575
Posted By scalabrin
Please, contact the contact author, he will...

Please, contact the contact author, he will surely help you!

About installation, strange, I was easily able to install it myself, even on my home without asking for any system path.
Forum: De novo discovery 07-27-2012, 05:31 AM
Replies: 4
Views: 3,037
Posted By scalabrin
Simply because AllPaths turned out to be one of...

Simply because AllPaths turned out to be one of the best assemblers in Assemblathon1 and in GAGE!

But I also had some experience with other assemblers and I am not that exicted either in terms of...
Forum: De novo discovery 07-27-2012, 04:11 AM
Replies: 4
Views: 3,037
Posted By scalabrin
Anybody able to help me? Is there any way to...

Anybody able to help me?

Is there any way to cheat AllPaths-LG to make it work with short insert (300-800bp) libraries?
Forum: Bioinformatics 07-13-2012, 08:52 AM
Replies: 4
Views: 2,632
Posted By scalabrin
Assembly merge?

Dear YT,

I would try merging the last 3 datasets first. I would call it assembly merge or assembly reconciliation!

One tool to do it, under development in our lab is GAM (Genome Assembly...
Forum: De novo discovery 07-10-2012, 07:45 AM
Replies: 4
Views: 3,037
Posted By scalabrin
AllPaths-LG

I am trying to force AllPaths-LG to use my paired-end data with "standard" insert size of about 300bp.

As per documentation it does fail. But is there a way to fool AllPaths and pass it fragment...
Forum: Bioinformatics 03-13-2012, 04:10 AM
Replies: 2
Views: 2,478
Posted By scalabrin
you can also see rNA, it is mainly an aligner but...

you can also see rNA, it is mainly an aligner but does also a good job on sequence filtering (you need to construct a database of sequences to be filtered) and quality trimming...
Forum: Bioinformatics 02-04-2012, 11:06 PM
Replies: 4
Views: 8,567
Posted By scalabrin
Perhaps you need to tell Java to use your memory...

Perhaps you need to tell Java to use your memory (Java heap space), if I remember correctly Java allocates only 1Gb of memory if you don't instruct it differently.
You should use the option -Xmx
...
Forum: Bioinformatics 01-04-2012, 06:41 AM
Replies: 4
Views: 8,567
Posted By scalabrin
Hi Doug, I just had the same problem and...

Hi Doug,

I just had the same problem and solved it with -XX:MaxPermSize=512m

As you already tried with 1g, it looks like you just need to increase it further... was the 4g enough?
Forum: Bioinformatics 08-22-2011, 06:57 AM
Replies: 5
Views: 4,804
Posted By scalabrin
We are working on a tool, GAM...

We are working on a tool, GAM http://services.appliedgenomics.org/software/gam/, that does that.
At the moment it is Sanger based but we are close to a NGS release. In the first version it will...
Forum: De novo discovery 08-22-2011, 05:50 AM
Replies: 82
Views: 46,882
Posted By scalabrin
just a quick update on GAM, at the moment it is...

just a quick update on GAM, at the moment it is Sanger based only but we are modifying it to accept NGS (bam) files as well!

http://services.appliedgenomics.org/software/gam/
Forum: Bioinformatics 08-22-2011, 05:36 AM
Replies: 10
Views: 9,575
Posted By scalabrin
Hi, GAM was sanger based and currently supports...

Hi,
GAM was sanger based and currently supports assembly from Arachne and PCAP only. We are working on a NGS version that supports bam files.
Forum: Service Providers 08-03-2011, 07:46 AM
Replies: 162
Views: 169,131
Posted By scalabrin
Dear dottomarco, to be honest I would say you...

Dear dottomarco,
to be honest I would say you are not the Italian leading company neither on Sanger nor on NGS sequencing. I apologize for the rude message but you are damaging IGA (Istituto di...
Forum: Bioinformatics 07-06-2011, 01:21 AM
Replies: 65
Views: 16,183
Posted By scalabrin
2 missing reads

>>> STEP 1: reducing files

READS FILE:
/path/tmp/1309943569477/sample10.sam was reduced to /path/tmp/1309943569477/NGSrich_sample10_pinot.5066.txt

in the second file there is one line less,...
Forum: Bioinformatics 07-06-2011, 01:07 AM
Replies: 65
Views: 16,183
Posted By scalabrin
Bug and bam supported in new version

Wig files are not correctly computed in step 5 if underscores are present in the path (I checked with and without) but statistics do not change (conversely to what I supposed):

>>> STEP 5:...
Forum: Bioinformatics 07-05-2011, 04:27 AM
Replies: 65
Views: 16,183
Posted By scalabrin
Bugs

1) I got two reads less than expected (as chariko did)
2) Mean coverage looks suspicious. At least in one sample where I expected about 50x coverage I got 501x coverage...
3) On target does not...
Forum: Bioinformatics 06-29-2011, 09:45 AM
Replies: 1
Views: 1,423
Posted By scalabrin
I have just seen Yandell's presentation at The...

I have just seen Yandell's presentation at The biology of genomes meeting (CSHL) and it looks very promising, apparently working on both rare and common diseases.

He hasn't tested any cancer data....
Forum: Service Providers 03-04-2010, 08:23 AM
Replies: 162
Views: 169,131
Posted By scalabrin
Service in Europe

IGA (Institute of Applied Genomics)
http://www.appliedgenomics.org/
Italy, Europe

Open to scientific collaborations and service provider: Illumina / Bioinformatics.
Forum: Bioinformatics 11-02-2009, 01:36 PM
Replies: 27
Views: 10,970
Posted By scalabrin
You might read this: ...

You might read this:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648799/?tool=pubmed

Parallel short sequence assembly of transcriptomes
Benjamin G Jackson, Patrick S Schnable, and Srinivas...
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