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Raw reads were trimmed using Trim_Adaptor application (non Open source application) with the minimum clip length fixed at 6 nucleotides.
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The parameters (minimum overlap identity and length, seed length, step and count, and alignment difference and identity scores for newbler; minimum overlap identity and length; and clip length and stringency for MIRA) were automatically optimized for contig length by using a genetic algorithm with the default parameters used as starting points, a population size of 10, and 10 generations.
Reads from all life stages were pooled and assembled using the Trinity package [ 17] version r2012-10-05 with the jellyfish k-mer method; RF strand-specific library type; jaccard clip; 200 bp minimum contig length; and paired_fragment_length of 400 bp.
RNA-seq reads from in vitro mycelia were assembled using Trinity v r2011-11-26 [ 67] with standard parameters, jaccard clip on and a minimum contig length of 200 bp.
The fastx_clipper program was used to remove the Illumina paired-end adapter sequences requiring a minimum sequence length of 15 nt after clipping.
Minimum length is 600 words; maximum length is 800 words.
These C-tails were removed using the "clip adapter sequences script" with the 3' adapter set to CCCCCCCCCCCCCCCCCCCCCCCCCC and the minimum read length set to 26.
minimum description length criterion.
minimum description length.
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The minimum focal length is 5.1 mm and the max is 12.8 (about a 24-60mm equivalent on a 35mm frame).
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