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The read median insert size (Supplementary Figure S3A), aligned ratio of pass filter reads (Supplementary Figure S3B), and ratio of chimeric pairs (Supplementary Figure S3C) were significantly poorer in FFPE than FF specimens (p = 1.798e−09, 3.618e−09, and 1.330e−08, respectively).
Median insert size was 200 bp.
The median insert size between paired-end reads ranged from 131 to 151 bases per sample.
The median insert size, measured after removal of nonjumping and chimeric outliers, was 35.7 kbp.
Median insert size of PE data was 335 (with a median absolute deviation of 21), whereas median insert size of MP data was 2473 (with a median absolute deviation of 704).
On the Illumina platform, we generated 102,278,116 paired 79-mers with a median insert size of 340bp.
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Based on paired read mapping, the libraries showed median insert sizes of 170 bp (PE), 3 kb, 5 kb, 8 kb, 15 kb, 20 kb, and 25 kb.
For each species, ~20 million paired-end sequence reads of 100 bp were generated from sequencing libraries with median insert sizes of 760 bp to 910 bp (Additional File 1: Table S1).
Briefly, the gDNA was fragmented and subjected to end-repair, A-tailing, ligation of adaptors including sample-specific barcodes and size-selection to obtain a library with median insert-size around 300 bp.
The final assembly contained 27,377 reads: 12,990 small insert reads (average insert size ≅ 4200 bp), 7,364 large insert reads (average insert size ≅31,650 bp) and 7,023 PCR-based reads.
The draft phase involved two clone libraries, one small insert library (2200 bp average insert size) and one medium insert library (6289 bp average insert size).
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