Scaffold_builder is software to order contigs generated by draft sequencing along a reference sequence. Gaps are filled with N’s and small overlaps are aligned with Muscle and the consensus created with IUPAC codes. Scaffold_builder can help in the assembly and annotation of genomes by revealing what is missing and allowing targeted sequencing to close those gaps.
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Source Code Biol Med. 2013 Nov 22;8(1):23. doi: 10.1186/1751-0473-8-23.
Combining de novo and reference-guided assembly with scaffold_builder.
Silva GG1, Dutilh BE, Matthews TD, Elkins K, Schmieder R, Dinsdale EA, Edwards RA.