All read datasets originated from DNA extracted from the same individual fish, designated NEAC_001, a wild-caught male specimen of the North-East Arctic population, sampled with the main purpose for sequencing initiative of the Atlantic cod genome and described in detail in [5 ]. We always strive to limit the effect of our sampling needs on populations and individuals. This individual was sampled in connection with a research survey conducted by Norwegian Institute for Water Research as part of part of larger hauls for stock assessments. The fish were humanely sacrificed by administration of other sedatives before sampling in accordance with the guidelines set by the ’Norwegian consensus platform for replacement, reduction and refinement of animal experiments’ (www.norecopa.no ). See Additional file 1 : Table S1 for an overview of different DNA datasets generated from this individual.
Roche/454 reads were sequenced as described previously [5 ]. The Roche/454 software gsRunProcessor version 2.6 was used to redo basecalling for all sequencing runs generated for the NEAC_001 sample [5 ].
One hundred eighty bp insert size and 300 bp insert size libraries were constructed with Illumina DNA paired end sample preparation reagents and sequenced at the Norwegian Sequencing Centre. The 5 kbp insert size libraries were prepared with the Illumina Mate Pair gDNA reagents and sequenced at the McGill University and Génome Québec Innovation Centre. All Illumina libraries were sequenced on the HiSeq 2000 using V3 chemistry 100 bp paired end reagents.
PacBio SMRT sequencing was performed on PacBio RS instrument (Pacific Biosciences of California Inc., Menlo Park, CA, USA) at the Norwegian Sequencing Centre (www.sequencing.uio.no/ ) and at Menlo Park. Long insert SMRTbell template libraries were prepared at NSC (10 kbp insert size) and Menlo Park (22 kbp insert size) according to PacBio protocols. In total, 147 SMRT-cells were sequenced using C2 and XL polymerase binding and C2 and XL sequencing kits with 120 min acquisition. Approximately 7.6 Gb of library bases were produced from 10 kb SMRTbell libraries sequenced on 102 SMRT cells using C2/C2 chemistry (average polymerase read length of 3 kb). The 22 kb SMRTbell library was sequenced using C2/XL (22 SMRT cells, average polymerase read length of 4.5 kb) and XL/XL (23 SMRT cells, average polymerase read length of 5 kb) chemistry producing 5.5 Gb of library bases.
Roche/454 reads were sequenced as described previously [5 ]. The Roche/454 software gsRunProcessor version 2.6 was used to redo basecalling for all sequencing runs generated for the NEAC_001 sample [5 ].
One hundred eighty bp insert size and 300 bp insert size libraries were constructed with Illumina DNA paired end sample preparation reagents and sequenced at the Norwegian Sequencing Centre. The 5 kbp insert size libraries were prepared with the Illumina Mate Pair gDNA reagents and sequenced at the McGill University and Génome Québec Innovation Centre. All Illumina libraries were sequenced on the HiSeq 2000 using V3 chemistry 100 bp paired end reagents.
PacBio SMRT sequencing was performed on PacBio RS instrument (Pacific Biosciences of California Inc., Menlo Park, CA, USA) at the Norwegian Sequencing Centre (
Free full text: Click here
