Open Access Highly Accessed Research article

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers

Michael A Quail*, Miriam Smith, Paul Coupland, Thomas D Otto, Simon R Harris, Thomas R Connor, Anna Bertoni, Harold P Swerdlow and Yong Gu

Author Affiliations

Wellcome Trust Sanger Institute, Hinxton, UK

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BMC Genomics 2012, 13:341  doi:10.1186/1471-2164-13-341

Published: 24 July 2012

Additional files

Additional file 1: Table S1:

Statistics for Illumina Sequencing Runs. Table S2. Statistics for Ion Torrent Sequencing Runs. Table S3. Statistics for PacBio Sequencing Runs.

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Additional file 2: Figure S1:

Comparison of the outcome of sequencing using libraries prepared using enzymatic shearing (green line) and physical shearing (blue line) on the Ion Torrent PGM. A) The percentage of the P. falciparum genome covered at different read depths; B) The number of bases covered at different depths; C) Sequence representation versus GC content. Figure S2. Genome coverage uniformity plots for 15x depth randomly normalized sequence coverage from sequencing libraries prepared using standard and Nextera Library preparation methods. A) The percentage of the B. pertussis genome covered at different read depths; B) The number of bases covered at different depths for B. pertussis; C) The percentage of the S. aureus genome covered at different read depths; D) The number of bases covered at different depths for S. aureus; E) The percentage of the P. falciparum genome covered at different read depths; and F) The number of bases covered at different depths for P. falciparum. Figure S3. Sequence representation versus GC content for 15x depth randomly normalized sequence coverage from sequencing libraries prepared using standard and Nextera Library preparation methods. Genome coverage uniformity plots for 15x depth randomly normalized sequence coverage from sequencing libraries prepared using the Illumina Nextera Library preparation kit (blue line) compared to those prepared using a standard Illumina library preparation with Kapa HiFi for library amplification (green line), on: A) B. pertussis; B) S. aureus and C) P. falciparum genomes. Figure S4. Sequence representation versus GC content for 15x depth randomly normalized sequence coverage from the sequencing platforms tested, on: A) B. pertussis; B) and C) P. falciparum genomes.

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Additional file 3: Table S4:

Comparison of sequence coverage for data generated with PacBio, PGM and MiSeq across the P. falciparum genome. Reads from randomly normalized 15x datasets were remapped with SMALT to have a uniform mapping score. To analyse the utility of long reads, read length and mate-pair read analysis was also performed on 15x datasets comprising PacBio reads longer than 620 bases, and MiSeq paired- and single-end datasets with 150-base, 100-base and 50-base read lengths.

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Additional file 4: Table S5:

Ratios of the occurrence of quality loss after specific sequence triplets following the GGC motif. For each strand, the occurrence and subsequent mapping quality is tabulated for the GGC motif and for comparison another GC-rich motif GCC and the neutral motif ATG. Ratios are then given for the sequence quality observed on the forward and reverse strands following the GGC triplet and ratios of mapping quality on the same strand following GCC and ATG triplets when compared to the GGC triplet.

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Additional file 5: Table S6:

SNP detection statistics for S. aureus datasets versus S. aureus USA300_FPR3757.

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