Could anyone suggest me good whole genome alignment tools?

[abysslover]

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

[scalabrin]

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

or mummer package with nucmer (but this is slow).

[milo0615]

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.

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

[abysslover]

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

[divya]

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

[GenoMax]

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"?

[divya]

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

[GenoMax]

At a minimum PICARD PATH would need to be set to /usr/bin. Start with that.