In order to take platform dependent sequencing artifacts into consideration, 454 and Illumina reads were assembled separately using different assembly programs.
These two data sets were assembled separately using the EST sequence assembler geneDistiller Scheibye-Alsing KK et al: EST assembly with genedistiller, submitted), resulting in, respectively, 420 and 1,207 contigs and 1,205 and 4,438 singlets.
These two data sets were assembled separately using the EST sequence assembler geneDistiller Scheibye-Alsing KK et al: EST assembly with genedistiller, submitted), and the resulting Heliconius contigs and singlets are available in additional files 4 and 5 respectively.
The reads from each library were assembled separately by Roche Newbler (GS-assembler) version 2.3.
Using MIA Mapping Iterative Assemblerr available at https://github.com/udo-stenzel/mapping-iterative-assembler, last accessed December 2013) mitochondrial genomes were assembled separately for each library.
Illumina readseq reads from each cultivar (Atlantic, Premier Russet, and Snowden) were assembled separately using the Velvet assembler [ 39] in the paired-end mode with a hash length of 31 and a minimum contig length of 150 bp.
Each library sequence set (Table 1) was assembled separately to obtain specific UniGene assemblies for every gene library and every pine species (Table 2); P. pinaster comprehensive assembly was also performed with MIRA3 with mixed 454-Sanger settings.
The BE and BEY sequences were assembled separately by using GS de novo assembler.
The remaining reads for each of the five libraries were assembled separately using the GS de novo assembler 2.6 (454 Life Sciences/Roche Diagnostics) with the -cdna option.
After removal of adaptor sequences, ambiguous reads, and low quality reads (Q20 <20) from the combined (41 SRA) datasets, clean reads with same sequencing lengths were assembled separately, and then the resultant partial assembly further assembled together.
