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Old 08-06-2014, 08:19 AM   #1
dsenalik
Carrot Scientist
 
Location: Madison WI USA

Join Date: Nov 2009
Posts: 42
Default Definition of Scaftig

There appears to be a lack of a clear definition of the term "scaftig".
How do you use this term? Is there a good definition somewhere?

I think it should have a very definite distinction from the term contig, and I would define it as
"All portions of a final assembly consisting of contiguous sequence, with sequences split at every occurrence of gaps of unknown bases (Ns)."

For example, if my final assembly is
>C1020304
ACTGTGATCG
>scaffold1234
CGTCGATCnnnnnnCGATCGATnCATGCA

My scaftigs are
>scaftig1
ACTGTGATCG
>scaftig2
CGTCGATC
>scaftig3
CGATCGAT
>scaftig4
CATGCA

Additionally, you could use the term "scaffold scaftigs" if you wanted to make clear that the left-over contigs are not to be included in the set of scaftigs.

References
I have found only a few somewhat inconsistent definitions available, in order of publication:
  1. "A scaftig refers to a continuous sequence formed by multiple initial contigs lined up in a scaffold with putative sequence overlaps."
    State of the art de novo assembly of human genomes from massively parallel sequencing data
    Hum Genomics. 2010; 4(4): 271–277. (April 1, 2010)
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3525208/
    Can sequence not in a scaffold be considered scaftigs? This definition would imply no.
  2. "New word of the day: #scaftigs RT @assemblathon 'scaftigs' intra-scaffold gaps between contigs. #gaw"
    Twitter (March 15, 2011)
    https://twitter.com/SCEdmunds/status/47730194563342336
    This strangely seems to define the gaps rather than the sequence. I include this because there are few definitions to be found.
  3. "scaftigs can be constructed by extracting the contiguous sequences that lack unknown bases (Ns)."
    Mende DR, Waller AS, Sunagawa S, Järvelin AI, Chan MM, et al. (2012) Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data. PLoS ONE 7(2): e31386. doi:10.1371/journal.pone.0031386 (February 23, 2012)
    http://www.plosone.org/article/info%...l.pone.0031386
    This is closest to my definition
  4. "The resulting high-quality reads were assembled into scaftigs using SOAPdenovo 1.05 and genes predicted on scaftigs longer than 500 nt using MetaGeneMark v1.0"
    Country-specific antibiotic use practices impact the human gut resistome
    Genome Res. 2013. 23: 1163-1169 (April 8, 2013)
    http://genome.cshlp.org/content/23/7/1163.full
    Supplementary Materials and Methods
    I would call these contigs, they are the primary product of an assembly.
  5. ABySS version 1.5.0 introduced a command (May 1, 2014)
    "New command, `scaftigs`. Breaks scaffold sequences at 'N's and produce a scaftigs.fa file."
    http://www.bcgsc.ca/platform/bioinfo...releases/1.5.0

Other references that I found do not define the term.
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Old 08-19-2014, 07:17 AM   #2
vitorpiro
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Location: Berlin

Join Date: Aug 2012
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Default

If I understand well, scaftigs are the contigs (contiguous sequences) from scaffolds, right? (Can be interpreted as the same set of the original contigs without the ones that are not included in any scaffold).
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