<![CDATA[BOL: Tadpole: an assembler, error-corrector, and read-extender]]> https://bioinformaticsonline.com/bookmarks/view/40895/tadpole-an-assembler-error-corrector-and-read-extender? https://bioinformaticsonline.com/bookmarks/view/40895/tadpole-an-assembler-error-corrector-and-read-extender Tue, 04 Feb 2020 23:35:40 -0600 https://bioinformaticsonline.com/bookmarks/view/40895/tadpole-an-assembler-error-corrector-and-read-extender <![CDATA[Tadpole: an assembler, error-corrector, and read-extender]]> Tadpole is a kmer-based assembler, with additional capabilities of error-correcting and extending reads. It does not do any complicated graph analysis or scaffolding, and therefore, is not particularly good for diploid organisms. Tadpole is very conservative and optimized for correctness rather than length; which is to say, it stops at every branch, and condenses every repeat. Also, it does not currently do scaffolding.

 

To error-correct reads:
tadpole.sh in=reads.fq out=corrected.fq mode=correct

To extend reads by 50bp in each direction:
tadpole.sh in=reads.fq out=extended.fq mode=extend el=50 er=50

To error-correct and extend at the same time, using a kmer length of 62:
tadpole.sh in=reads.fq out=extended.fq mode=extend el=50 er=50 k=62 ecc=t

 

More at http://seqanswers.com/forums/showthread.php?t=61445

Address of the bookmark: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/tadpole-guide/

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