SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Is there any good statistic way or tools to compare the read count owwa Bioinformatics 7 04-20-2014 04:21 PM
Good poly-A filtering rules or tools ysnapus Bioinformatics 0 07-03-2013 11:59 AM
Bowtie alignment for ChIP-seq: good alignment for input but not for ChIP sample nico_z Bioinformatics 2 03-20-2013 11:19 AM
Comparison of alignment tools genbio64 Bioinformatics 6 07-18-2011 11:57 AM

Reply
 
Thread Tools
Old 06-23-2015, 10:43 AM   #1
abysslover
Member
 
Location: Germany

Join Date: Jul 2013
Posts: 13
Question Could anyone suggest me good whole genome alignment tools?

Hi, I've been working on population genetics with 1001 genome datasets (the size of A. thaliana genome is around 120 mb, as you know).

As a first attempt, I would like to perform the whole genome alignment for three genome assemblies to find synteny blocks among these accessions. The quality of each genome assembly is good in terms of N50, the number of scaffolds, and so on.

I was told about progressive cactus, which can perform the whole genome alignments. For few accessions, the tool seems to work well. The only problem is the runtime of alignments since I am going to put more datasets in the set of comparisons. According to my colleague, the progressive cactus is somehow slow.

Are there any time-efficient and user-friendly tools around for the whole genome alignment, which can deal with long reads or genome assemblies? For our cluster environment, the total memory consumption should be less than 1Tb.
Your suggestion would be greatly appreciated.

Regards,
=============================
PhD Student

Max Planck Institute for Developmental Biology
Department of Molecular Biology
Spemannstraße 37-39,
D-72076 Tuebingen, Germany

Last edited by abysslover; 06-23-2015 at 10:54 AM.
abysslover is offline   Reply With Quote
Old 06-30-2015, 05:26 AM   #2
scalabrin
Member
 
Location: Udine, Italy

Join Date: Jul 2009
Posts: 22
Default

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

or mummer package with nucmer (but this is slow).
scalabrin is offline   Reply With Quote
Old 07-10-2015, 04:47 PM   #3
milo0615
Member
 
Location: Walnut, California

Join Date: Dec 2012
Posts: 39
Default

Hi abysslover,

Were you able to align the genomes against each other? I currently have two plant de novo assemblies generated by Abyss and a reference genome from a closed related specie. I would like to align them against each other to and compare any genetic differences between the two. Can you please share what tools you used for the alignment and visualization? I would really appreciate your help.

Quote:
Originally Posted by abysslover View Post
Hi, I've been working on population genetics with 1001 genome datasets (the size of A. thaliana genome is around 120 mb, as you know).

As a first attempt, I would like to perform the whole genome alignment for three genome assemblies to find synteny blocks among these accessions. The quality of each genome assembly is good in terms of N50, the number of scaffolds, and so on.

I was told about progressive cactus, which can perform the whole genome alignments. For few accessions, the tool seems to work well. The only problem is the runtime of alignments since I am going to put more datasets in the set of comparisons. According to my colleague, the progressive cactus is somehow slow.

Are there any time-efficient and user-friendly tools around for the whole genome alignment, which can deal with long reads or genome assemblies? For our cluster environment, the total memory consumption should be less than 1Tb.
Your suggestion would be greatly appreciated.

Regards,
=============================
PhD Student

Max Planck Institute for Developmental Biology
Department of Molecular Biology
Spemannstraße 37-39,
D-72076 Tuebingen, Germany

Thank you,
-Milo
milo0615 is offline   Reply With Quote
Old 07-14-2015, 02:04 AM   #4
abysslover
Member
 
Location: Germany

Join Date: Jul 2013
Posts: 13
Default

Hi, Milo,

I am actually developing a whole genome alignment tool. Though scalabrin replied to my question, Denom is not fit for my purpose. I was able to align those scaffolds against each other by my own alignment algorithm. It reports the positions in the scaffolds and in the reference genome at the same time. I have not implemented a visualization tool yet.

cheers,
Euncheon

Last edited by abysslover; 07-14-2015 at 03:17 AM.
abysslover is offline   Reply With Quote
Old 01-03-2017, 04:02 AM   #5
divya
Junior Member
 
Location: india

Join Date: Nov 2016
Posts: 5
Default

Hello

I am a new user of IMR/DENOM, i have its all executable file and also install all needed softwares and its project file made, but it is not working. an error shows:-

Start at: Tue Jan 3 17:04:13 2017
Script PATH: /home/genomics2/tools/imrdenom/scripts/x86_64/
PICARD PATH: /home/genomics2/tools/imrdenom/external/
Can't find the Picard, please install it first.

But picard is executable in terminal.
Please help me how do I proceed.

Thanks
divya is offline   Reply With Quote
Old 01-03-2017, 04:54 AM   #6
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,576
Default

Quote:
Originally Posted by divya View Post
Hello

I am a new user of IMR/DENOM, i have its all executable file and also install all needed softwares and its project file made, but it is not working. an error shows:-

Start at: Tue Jan 3 17:04:13 2017
Script PATH: /home/genomics2/tools/imrdenom/scripts/x86_64/
PICARD PATH: /home/genomics2/tools/imrdenom/external/
Can't find the Picard, please install it first.

But picard is executable in terminal.
Please help me how do I proceed.

Thanks
Is PICARD path correct? What happens if you run "which picard"?
GenoMax is offline   Reply With Quote
Old 01-03-2017, 05:48 AM   #7
divya
Junior Member
 
Location: india

Join Date: Nov 2016
Posts: 5
Default

Thanks for your reply..

picard is in /usr/bin/picard

I give command
imr easyrun -m bwa -q /home/genomics2/Desktop/divya/wgsdata/top/wgs.fastq

Last edited by divya; 01-03-2017 at 05:54 AM.
divya is offline   Reply With Quote
Old 01-03-2017, 07:16 AM   #8
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,576
Default

At a minimum PICARD PATH would need to be set to /usr/bin. Start with that.
GenoMax is offline   Reply With Quote
Reply

Tags
whole genome mapping

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 10:25 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO