User:Genomesequencer/Sandbox: Difference between revisions
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{{Infobox Software |
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| name = Consed |
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| developer = David Gordon |
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| operating system = UNIX, Linux, Mac OS X |
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| genre = [[Bioinformatics]] |
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| license = free for academic users |
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| website = http://bozeman.mbt.washington.edu/consed/consed.html |
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}} |
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'''Consed'''<ref name="Gordon1998">{{cite journal |author=Gordon D, Abajian C, Green P |title=Consed: A Graphical Tool for Sequence Finishing |journal= Genome Research |volume=8 |pages=195-202 |year=1998}}</ref> is a program for viewing, editing, and finishing DNA [[sequence assembly|sequence assemblies]]. Originally developed for sequence assemblies created with [[phrap]], recent versions also support other sequence assembly programs like Newbler. |
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=== History === |
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Consed was originally developed as a contig editing and finishing tool for large-scale cosmid shotgun sequencing in the [[Human Genome Project]]. At genome sequencing centers, Consed was used to check assemblies generated by [[phrap]], solve assembly problems like those caused by highly identical repeats, and finishing tasks like primer picking and gap closure. |
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Development of Consed has continued after the completion of the [[Human Genome Project]]. Current Consed versions support very large projects with millions of reads, enabling the use with newer sequencing methods like [[454 Life Sciences|454 sequencing]] and [[Solexa]] sequencing. Consed also has advanced tools for finishing tasks like automated primer picking <ref name="Gordon2001">{{cite journal |author=Gordon D, Desmarais C, Green P |title=Automated Finishing with Autofinish |journal= Genome Research |volume=11 |pages=614-625 |year=2001}}</ref> |
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===References=== |
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{{reflist}} |
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=== External links === |
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*[http://bozeman.mbt.washington.edu/consed/consed.html Consed homepage] |
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{{bioinformatics-stub}} |
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== Other Software == |
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*[[Phred quality score|Phred]] |
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*[[phrap|Phrap]] |
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[[Category:Bioinformatics]] |
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[[Category:Computational_science]] |
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