The mango transcriptome assembly was created and characterized by application of RNA-seq to fruit-peel samples.
Cationic nano- and microporous coatings and particle assemblies were created by spray-coating with cationic calcium carbonate precipitated in the presence of PDADMAC.
Individual BAC assemblies were created with PHRAP [ 74] and assessed for contiguity.
Two additional VELVET assemblies were created with k-mer sizes 21 and 31, with read category set to shortPaired of the raw read data.
A series of 7 separate Velvet-Oases assemblies were created specifying ins_length 161 -ins_length_sd 150 and using k-mers ranging from 33 to 69 (with steps of 6), then these were merged using the Oases-Merge function (K = 27) specifying -min_trans_lgth 200.
Assemblies were created using k-mer sizes of 31, 41, 51 and 61.
De novo assemblies were created using the Roche Newbler (v 2.3) software package and the resulting contigs were annotated using NCBI's Prokaryotic Genomes Automatic Annotation Pipeline [PGAAP, [ 36]].
The de novo transcriptome assemblies were created using the de Bruijn graph-based assembler (Trinity release 2013-02-25) (Gralherr et al. 2011).
Seven different assemblies were created with identity values of 75, 80, 85, 90, 95, 97 and 99 in a minimum overlap length of 40 bp for each of the samples plus an extra sample with half of a 454 run of N. sylvesteris and half of a run of N. tomentosiformis.
Three alternative assemblies were created, set 1 was carried out using the Abyss assembler at TGAC, set 2 was created by Genostar, Montbonnot, France and set 3, from SequenceAnalysis.co.uk, Norwich, UK, corresponded to the second assembly with contaminating contigs of low coverage removed.
