Scaffolds Aligment
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10.6 years ago
Matteo ▴ 220

Hi all,

I have the sequence of a scaffold in fasta format and i would like to get the chromosome coordinates (boundaries of the scaffold) on the target genome.

Are there any tools to perform this issue?

I have tried Blast but the scaffold spans over different contigs and i cannot retrieve the left and right end coordinates over the genome.

Greetings,

Matteo

scaffolding alignment genome • 5.6k views
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probably you can use BLAT utility from UCSC [ URL : http://hgdownload.cse.ucsc.edu/downloads.html ]

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I'm working on Arabidopsis scaffolds. Plants are not covered in UCSC :(

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Ashwin refers to software available for download from UCSC, not the genome browser.

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local alignment is not required, you need semi-local (global local) alignment. If it's only one scaffold glsearch should do.

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No, for contig alignment, it is crucial to do local alignment. There are structural variations and misassemblies. Glocal alignment will miss all these interesting events.

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yes, you are right

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10.6 years ago
lh3 33k

For bacteria and arabidopsis, mummer could be a good candidate. You may also try bwa-sw, which is designed for accurate alignment. Blat also works, but it is slow for long contigs. It may miss some split contig in the presence of repeats, too.

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Thanks! Mummer is what i was looking for.

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10.6 years ago
biomed.lu ▴ 20

http://contiguator.sourceforge.net/ This tool will help you to map your scaffolds/contigs back to ref genome and output the chromosome coordinates...

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Can contiguator theoretically works for non-bacterial genomes? I've take a glimpse to the software and seems that it needs overlapping contigs. Unfortunately i'm dealing with non-overlapping scaffolds.

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I, i'm the creator of contiguator: i've developed the tool to cope with bacterial genomes, but it may work well also for non-bacterial genomes. If you can give it a try we could even try to improve it in order to work better with those genomes. Let me know :)

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