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
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
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