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isovic / graphmap

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/graphmap2
MIT License
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Merging contigs #25

Open ursky opened 8 years ago

ursky commented 8 years ago

I am trying to merge my contigs by closing the gaps with long reads. I ran graphmap in hopes of finding reads that overlap two different contigs (which would allow me to merge these), and got a mhat output that looks promising. However, I am having a hard time finding software to actually take in this file to merge the contigs. Is this something that anyone encountered, and what tools would you recommend?

Thank you!

nnnagara commented 8 years ago

Are you trying to scaffold contigs? If so, OPERA-LG can do this for you,

Niranjan

From: "German V. Uritskiy" notifications@github.com<mailto:notifications@github.com> Reply-To: isovic/graphmap reply@reply.github.com<mailto:reply@reply.github.com> Date: Wednesday, 25 May, 2016 10:03 PM To: isovic/graphmap graphmap@noreply.github.com<mailto:graphmap@noreply.github.com> Subject: [isovic/graphmap] Merging contigs (#25)

I am trying to merge my contigs by closing the gaps with long reads. I ran graphmap in hopes of finding reads that overlap two different contigs (which would allow me to merge these), and got a mhat output that looks promising. However, I am having a hard time finding software to actually take in this file to merge the contigs. Is this something that anyone encountered, and what tools would you recommend?

Thank you!

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