Trinity was run using the following parameters: the fixed default k-mer size of 25 and a minimum contig length of 200 bp.
For values of k in (20, 30, 40,..., 80), IDBA-UD will attempt to assemble its partition (via de Bruijn graph methods) using k-mers of size k, and will then merge and extend results from all passes to produce a final assembly of that partition (requiring a minimum contig length of 100 nucleotides).
De novo genome assembly was done by de novo assembly tool in CLC Genomics Workbench with mismatch cost, insertion cost, deletion cost, similarity fraction, length fraction, and minimum contig length of 2, 3, 3,0.9, 0.9, and 1000, respectively (all other parameters were set as default or auto-detect mode).
Standard parameters were used and the minimum contig length was 300 bp.
De novo assembly of high quality data was accomplished using the CLC Genomics workbench 6.0 (Qiagen, USA) at default parameters (minimum contig length: 200, automatic word size: yes, perform scaffolding: yes, mismatch cost: 2, insertion cost: 3, deletion cost: 3, length fraction: 0.5, similarity fraction: 0.8).
Second, the contigs were assembled using CLC de novo assembler with the following optimized parameters: bubble size of 98, minimum contig length of 200, mismatch cost of two, deletion and insertion costs of three, length fraction of 0.9, and similarity fraction of 0.8.
Approximately 40 million Solexa (Illumina Inc., San Diego, CA, USA) sequenced ESTs were also included from the 'digital transcriptome' of B. napus lines TapidorDH and Ningyou7 [24], which was assembled using Velvet [25] with minimum contig length of 100 bp, coverage cut-off of five and k-mer value of 23, producing 29,956 contigs.
The minimum contig length was set to 200 bases.
The minimum contig length parameter was set to 70 bp.
We set the minimum contig length to 200 bp.
The minimum contig length was set at 100 bp.
