A new software for analyzing next-gen genomic data

[biofqzhao]

inGAP (Integrated Next-gen Genome Analysis Platform)

Please refer to the following link for detail.
http://sites.google.com/site/nextgengenomics/ingap

inGAP is an integrated platform for next-generation sequencing project, the core function of which is to detect SNPs and indels using a Bayesian algorithm.

(1) It does not have any read length restriction. It can handle 454 sequencing and/or Illumina Solexa sequencing and/or Sanger sequencing data sets.

(2) It can detect most small indels in either single-end or paired-end data sets. Using the simulated data sets, inGAP could successfully identify 85%-98% of small indels with high accuracy (>99%).

(3) It has a strong capability to identify variants based on a relatively divergent reference genome, which bring it to a much wider application other than resequencing projects.

(4) It provides a user-friendly graphic interface, through which users can browse, search, check, classify, and even edit the identified variants.

(5) It can be used to detect intraspecific polymorphisms (including SNPs and indels) based on a pairwise comparison of multiple whole genomes.

(6) It employs a global heuristic searching approach to layout contigs based on one or more reference genomes.

(7) It also provides a handful of bioinformatic tools for read simulation, mutation incorporation, format conversion, etc.

(8) It's slower than other SNP detection programs (e.g. MAQ, SOAP, Bowtie), because it employs BLAST or BLAT to map reads. It generally takes about 220 minutes for comparing 10 million 75bp Illumina reads against a 12Mb yeast reference genome on an 8-core DELL machine.

Any comments and suggestions are welcome.

[tebuffer]

Does the links work...?



The download link doesnt seem to work ......

[sklages]

http://schuster-2.bx.psu.edu:8888/MAMP/shared/ should work ...

I am interested in opinions ...

Sven

[tebuffer]

Failed to connect....

Failed to Connect

Firefox can't establish a connection to the server at schuster-2.bx.psu.edu:8888.
---------------------------

Safari can’t connect to the server.
Safari can’t open the page “http://schuster-2.bx.psu.edu:8888/MAMP/shared/” because Safari can’t connect to the server “schuster-2.bx.psu.edu”.

----------------------------

[sklages]

hmm, this link works fine with linux, unix, windows, FF, Chrome, IE, home, work ...
It seems this is a problem with your mac(?) .. Firewall?

cheers,
Sven

[MQ-BCBB]

links not working

Sven, the links are not accessible from my end either. I am curious to try, hope the issue gets resolved.

MQ

[tebuffer]

Works with my WIFI....

Hi Sven and MQ-BCBB

It works now... but with my WiFi... connection, Not with my Ethernet connection.
Not able to fix it even after fixing IPv6 to 4 and other stuff as I learned googling for this error...

For now I will settle with my WiFi...

Thanks,
TEB

[biofqzhao]

We have a new version of inGAP (v1.9.4) now, and linux32 is also supported. Please check http://sites.google.com/site/nextgengenomics/ingap for detail.

[tebuffer]

Great Tool

Hi Sven,

inGAP is a great NICE tool.
The interface is very impressive and intuitive.
inGAP gave the best first impression.
Thanks for sharing.

TEB.

[MQ-BCBB]

I was able to download and map 454 reads

Thank you making this tool available. It took much longer than expected; I will then explore results.

MQ

[qij]

Sven, thank you so much for your kind help, thanks MQ and TEB for using and testing inGAP, I am looking forward to your comments and suggestions.

Thanks and regards,
Ji

[sklages]

Dear biofqzhao, Ji,

I have used inGAP to map a few 454XLR reads on a known
bacterial genome, size~3.8Mb.

I have a few questions about the program:

Export consensus
How is the consensus calculated? If I align my dataset against
a known reference I usually want my reads to build the consensus
if there is some evidence that the data and the alignment is
correct. So when I export the consensus. it should be my aligned
read data. That's what I assume, is that correct?
What does a '.' (dot) really mean in the exported consensus?
Sometimes i find a dot where there is one-base-coverage,
sometimes there is no dot in such regions ...

Wouldn't it be a good idea to also show the consensus above
the alignment? Maybe in an editable manner?

Genes
I'd like inGAP to use a provided PTT file downloaded just
from NCBI for my genome of interest.
When opening my project, I get an error,

UNEXISTS: [..]CONTIG_1/genes.table

This is probably not the file I supplied as PTT file..
So what is the "genes" file for and how do I get/create it
and what is the PTT file for when I import the read data
and reference sequence at the very beginning? It doesn't
get displayed ...

Is there any chance to import (via file) and display some
other data, e.g. known SNPs?

Sorry for the somewhat dumb questions but I couldn't find
some more details on the website.

Nice software, I like this program, as it is possible to
use standard tools like 'blast' or 'blat'.

Thanks,
Sven

[biofqzhao]

Thank you for your comments and suggestions.

Dear biofqzhao, Ji,

I have used inGAP to map a few 454XLR reads on a known
bacterial genome, size~3.8Mb.

I have a few questions about the program:

Export consensus
How is the consensus calculated? If I align my dataset against
a known reference I usually want my reads to build the consensus
if there is some evidence that the data and the alignment is
correct. So when I export the consensus. it should be my aligned
read data. That's what I assume, is that correct?
What does a '.' (dot) really mean in the exported consensus?
Sometimes i find a dot where there is one-base-coverage,
sometimes there is no dot in such regions ...
Zhao's reply:
Ji will reply you on this issue.

Wouldn't it be a good idea to also show the consensus above
the alignment? Maybe in an editable manner?
Zhao's reply:
That's a good idea. We will display the consensus sequence in the alignment window in the next update.


Genes
I'd like inGAP to use a provided PTT file downloaded just
from NCBI for my genome of interest.
When opening my project, I get an error,

UNEXISTS: [..]CONTIG_1/genes.table

This is probably not the file I supplied as PTT file..
So what is the "genes" file for and how do I get/create it
and what is the PTT file for when I import the read data
and reference sequence at the very beginning? It doesn't
get displayed ...
Zhao's reply: inGAP can convert the GenBank file to a PTT format. You can find it in the "Tools" panel.


Is there any chance to import (via file) and display some
other data, e.g. known SNPs?
Zhao's reply: Yes. You can load other data (e.g. SNPs identified by MAQ) into inGAP, but the data requires a specific format. We will provide a detailed manual soon.

Sorry for the somewhat dumb questions but I couldn't find
some more details on the website.
Zhao's reply: We will provide a detailed manual soon.

Nice software, I like this program, as it is possible to
use standard tools like 'blast' or 'blat'.
Zhao's reply: Thank you. Although tools like 'blast' or 'blat' are much slower than those newly described algorithms, these classic tools indeed perform very well in mapping short reads.
Thanks,
Sven

[qij]

Thanks a lot for all these kind suggestions.

Dear biofqzhao, Ji,

I have used inGAP to map a few 454XLR reads on a known
bacterial genome, size~3.8Mb.

I have a few questions about the program:

Export consensus
How is the consensus calculated? If I align my dataset against
a known reference I usually want my reads to build the consensus
if there is some evidence that the data and the alignment is
correct. So when I export the consensus. it should be my aligned
read data. That's what I assume, is that correct?
What does a '.' (dot) really mean in the exported consensus?
Sometimes i find a dot where there is one-base-coverage,
sometimes there is no dot in such regions ...

Wouldn't it be a good idea to also show the consensus above
the alignment? Maybe in an editable manner?
The consensus is just the majority type of covered
nucleotides. The dots are deletions in consensus and are kept in the
last version just for helping one of my labmate to checking possible
frame-shifts. I have modified inGAP not to output dots anymore and
will update you when a new version is available.

It is really a good idea to display consensus in the alignment panel.
I will add this new feature ASAP.

Genes
I'd like inGAP to use a provided PTT file downloaded just
from NCBI for my genome of interest.
When opening my project, I get an error,

UNEXISTS: [..]CONTIG_1/genes.table

This is probably not the file I supplied as PTT file..
So what is the "genes" file for and how do I get/create it
and what is the PTT file for when I import the read data
and reference sequence at the very beginning? It doesn't
get displayed ...

Both GFF and PTT formats were acceptable in
the old version. inGAP will load the original gene file in the “data import”
step and distribute gene information to different contigs (the file
“genes.table” in each PROJECT\CONTIG_* folder).
It is wired to get an error info like “UNEXISTS: [..]CONTIG_1/genes.table”
if GFF or PTT file are imported in the “data import” step. Would you
please send me your PTT file so I can check in my computer?



Is there any chance to import (via file) and display some
other data, e.g. known SNPs?
For importing extra SNP files, alignment files (blast format,
etc.), please open the project and show the viewer first, then select
“navigation” panel -> “data” button, then you will get a small dialog which
shows the current data entries (or rows), in this panel, you can add,
remove, update existing entries, or change the order of them. When new
entry is loaded, say, a new SNP table, you can compare the new SNP
entry with the old one by clicking right mouse button on the reads panel
then select “entry coverage” popup item (below the “export consensus”
item).

The formats of new entries could be
One column format (just one column, each line gives a position)
120
240
…

Three column format (start, end, strand). “+” for plus strand and “-” for
minus
1 100 +
200 240 –
…

And also blastn tablar, PTT, GFF, mummer SNP, MAQ pileup, etc. A detailed
manual is definitely needed, I will do it after finish a few jobs from my boss.

Sorry for the somewhat dumb questions but I couldn't find
some more details on the website.

Nice software, I like this program, as it is possible to
use standard tools like 'blast' or 'blat'.

Thanks,
Sven

[bioinfosm]

any others who tried out the tool? feedback?
I was impressed by the claims and was wondering to check it out on a dataset that ran on MAQ previously..

Why limit to blat/blast! Those are too slow for so many reads.. and any heads-up on parallel version? I am waiting for the run to complete, to be able to compare to my MAQ results.