This assembly was run with a minimum match size of 19 nucleotides, match percentage of 93%, mismatch penalty of 18, and gap penalty of 30.
For this assembly, we used a minimum match size of 19 nucleotides, match percentage of 88%, mismatch penalty of 18, and gap penalty of 30.
Results from assemblies run in Seqman Ngen with different starting values for gap penalty, minimum match size, and mimimum match percentage.
The assembly was run with a minimum match size of 19 nucleotides, match percentage of 95%, mismatch penalty of 18, and gap penalty of 30 (further information on assembly is available from the authors by request).
De novo assembly of the remaining reads was run with a minimum match percentage of 93%, a minimum match size of 19 bp, and a gap penalty of 30.
We first executed a reference-based assembly utilizing a set of approximately 19,000 unigenes available for P. taeda using a minimum match percentage of 88%, a minimum match size of 19 bp, and a gap penalty of 30.
In general, as the minimum matching size increases, specificity rises and sensitivity falls.
We used a minimum consecutive match size of 25 bases, a minimum match percentage of 70%, and a match spacing of 15-mer tags.
A rapid, high stringency clustering was performed first, using the "Fast Assembler" module, with the following parameters: minimum match 90%, match size 25, match spacing 150, gap penalty 0, gap length penalty 0.7, end position mismatch 0, and minimum sequence length 50.
Assembly parameters were as follows: file format, BAM; mer Size, 21; mer skip query, 2; minimum match percentage, 93; maximum gap size, 6; minimum aligned length, 35; match score, 10; mismatch penalty, 20; gap penalty, 30; SNP calculation method, diploid bayesian; minimum SNP percentage, 5; SNP confidence threshold, 10; minimum SNP count, 2; minimum base quality score, 5.
These datasets were then assembled using the SeqMan Pro assembler of the Lasergene software package v8.0.2 (DNASTAR, Madison USA) with the following program parameters: match size, 50bp; minimum match percentage, 80%; minimum sequence length, 40 bp; gap length penalty, 0.70 and maximum mismatch end bases, 15.
