I have used velvet to assemble and scaffold a phage genome from Illumina paired end data and produced the velvet_asm.afg file. I would now like to use AMOS/Hawkeye to assess the quality of the assembly. However, I have imported the .afg file into Hawkeye but it does not contain any of the feature data and in the scaffold view the reads are all coloured grey indicating they are unpaired. Is there some step between the velvet .afg file and Hawkeye that I have missed out? How can I get Hawkeye to display the paired data?
I have searched various forums and not come up with an answer to this. Any help would be greatly appreciated
Regards, Matt
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Hi,
I have used velvet to assemble and scaffold a phage genome from Illumina paired end data and produced the velvet_asm.afg file. I would now like to use AMOS/Hawkeye to assess the quality of the assembly. However, I have imported the .afg file into Hawkeye but it does not contain any of the feature data and in the scaffold view the reads are all coloured grey indicating they are unpaired. Is there some step between the velvet .afg file and Hawkeye that I have missed out? How can I get Hawkeye to display the paired data?
I have searched various forums and not come up with an answer to this. Any help would be greatly appreciated
Regards, Matt