File	Tool	Assembly kmer	Level	Gap closing	Min Length (kb)
tomato-scaffolds.abyss.77.fasta	Abyss	77	scaffold	yes	0
tomato-scaffolds.abyss.77.gc.ov31.1kb.fasta	Abyss	77	scaffold	yes	1

For the nitty-gritty details, please refer to the supplemental material accompanying the publication below.

Citation:
Razali R, Bougouffa S, Morton MJL, Lightfoot DJ, Alam I, Essack M, Arold ST, Kamau AA, Schmöckel SM, Pailles Y, Shahid M, Michell CT, Al-Babili S, Ho YS, Tester M, Bajic VB and Negrão S (2018) The Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides
Insights Into Salinity Tolerance. Front. Plant Sci. 9:1402. doi: 10.3389/fpls.2018.01402

Solanum pimpinellifolium ‘LA0480’ DNA library construction, sequencing and assembly
The S. pimpinellifolium accession ‘LA0480’ was sequenced using the HiSeq 2000 Illumina platform at King Abdullah University of Science and Technology (KAUST). DNA was extracted from whole flowers of a single soil-grown plant ‘LA0480-ref’ using the Qiagen DNeasy Plant Mini Kit (Qiagen, Germany). Two 101 bp paired-end (PE) short-read libraries (139 and 332 bp mean insert length) and five 100 bp mate-pair libraries (2, 6, 8, 10 and > 10 kb insert length) were prepared using the NEBNext Ultra DNA Library Prep Kit and the Nextera Mate-pair Library Kit, respectively (New England Biolabs, UK).
 

 Adapter sequences, low-quality four nucleotide stretches of nucleotides, and low quality leading and trailing bases were removed with Trimmomatic v0.33 (Bolger et al., 2014b) and reads with a final length of less than 36 bp after trimming were discarded. Processed PE data were de novo assembled into contigs using ABySS (Simpson et al., 2009) with a k-mer length of 77, as determined by k-mer analysis. These contigs were scaffolded based on library size information from the PE read libraries, followed by a second round of scaffolding with mate pair data utilizing the ABySS pipeline. GapCloser (Luo et al., 2012) was used to close gaps in the assembled scaffolds.

Mitochondrial contigs are labelled  [location=mitochondrion].