[gnome7]

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.

Can you help me please to setting the parameters, like: contig length, min (match_len/read_len) and min alignment identity, window length, window step? Thank you very much.

[biofqzhao]

"contig length" indicates the minimal length for your reference sequences. If you are using a whole bacterial genome as a reference, you need not make any change here and just use the default value; if you are using a batch of contigs (which may come from a de novo assembler), you need to set up a minimal length, say, 1000 bp, for the downstream read mapping. The contigs smaller than this value would be discarded.

min (match_len/read_len) and min alignment identity: If you are mapping reads to a very close reference genome, just use the default value. But if you want to map reads to a much divergent species, please refine them as what you want. For example, if you are mapping repetitive reads to a reference transposase element, you can use a lower threshold.

Window length and window step: just use the default value.

Can you help me please to setting the parameters, like: contig length, min (match_len/read_len) and min alignment identity, window length, window step? Thank you very much.

[gnome7]

inGAP linux version

Dear biofqzhao,
in linux I can't set the parameters. Why?
Please, look at the image uploaded.

Thank you very much for your help,
gnome7

[sklages]

The image uploaded looks like Windows to me, not linux.
Nevertheless, certain parameters are only accessible if you use blast/blat.

cheers,
Sven

[kajsa]

inGAP manual and export sequence

Dear Zhao, Ji and everybody else,

This new new program inGAP looks very interesting. It was very easy to use and I was able to assemble some Illumina reads to a mitochondrial genome.

But I found it a little more difficult to analyse the result from the assembly in the AlignViewer. Especially without any proper manual.

I don't really understand how to export the consensus sequence of the assembled reads. Can you please explain how to do that?

Thank you!

Kajsa

[gnome7]

inGAP manual and export sequence

Dear all,
me too!

Thank you!

[biofqzhao]

Thanks for your interest. We are now updating inGAP, and some functions were disabled. I think all this stuff will be done in a few weeks.

Actually, you can write a script to extract consensus sequences based on the SNP table identified by inGAP and your reference sequence. Just as an alternative approach before the update.

Dear Zhao, Ji and everybody else,

This new new program inGAP looks very interesting. It was very easy to use and I was able to assemble some Illumina reads to a mitochondrial genome.

But I found it a little more difficult to analyse the result from the assembly in the AlignViewer. Especially without any proper manual.

I don't really understand how to export the consensus sequence of the assembled reads. Can you please explain how to do that?

Thank you!

Kajsa

[kajsa]

Okay, that's good. Could you make a new post here to tell us when you are finished with the updating?

[quicksand21]

too many contigs error

Hi,

I am trying to test out inGAP and am getting an error which states I have too many contigs (>= 1000). The program stops.

I am using Windows version.

Any ideas on what my issue is?

I am trying to align e. coli reads to a reference genome.

Thanks!

[JackieBadger]

Hi,

Hopefully I get a reply on here as my emails bounce back from the main author.

I want to use BLAT to align my EST contigs to a reference genome. For the reference genome all I have is fasta file, and for the ESTs I have a fasta and qual file. However when I go into mapping options, BLAT is blocked out. I need to use BLAT so that spice sites are identified, thus BLAST is not an option.

Do I need a gene file in order to use BLAT? I doubt it seeing as im pretty sure this is not needed in the original program.

Any ideas?

Thanks,

J

[biofqzhao]

I would suggest you to try BLAST, as there is no much difference between them when aligning ESTs to a reference sequence. In ingap, both aligners can only show you the best match, and the 2nd best spliced matches will be ignored. Maybe nucmer is a good option for you.

BTW, BLAT is disabled in the latest version of ingap.

Hi,

Hopefully I get a reply on here as my emails bounce back from the main author.

I want to use BLAT to align my EST contigs to a reference genome. For the reference genome all I have is fasta file, and for the ESTs I have a fasta and qual file. However when I go into mapping options, BLAT is blocked out. I need to use BLAT so that spice sites are identified, thus BLAST is not an option.

Do I need a gene file in order to use BLAT? I doubt it seeing as im pretty sure this is not needed in the original program.

Any ideas?

Thanks,

J

[JackieBadger]

Thanks for the reply