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Performance benchmark results of reimplemented flagstats versus stock version. (A) Results using the <t>GIAB</t> <t>HG002</t> Illumina 2x250 BAM file with an NVMe SSD array available on AWS. (B) Results using the rapid autopsy Bn2 sample BAM file with an NVMe SSD array available on AWS. (C) Results using the GIAB HG002 Illumina 2x250 BAM file with a Lustre distributed file system. (D) Results using the rapid autopsy Bn2 sample BAM file with a Lustre distributed file system.
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Performance benchmark results of reimplemented flagstats versus stock version. (A) Results using the GIAB HG002 Illumina 2x250 BAM file with an NVMe SSD array available on AWS. (B) Results using the rapid autopsy Bn2 sample BAM file with an NVMe SSD array available on AWS. (C) Results using the GIAB HG002 Illumina 2x250 BAM file with a Lustre distributed file system. (D) Results using the rapid autopsy Bn2 sample BAM file with a Lustre distributed file system.

Journal: Bioinformatics

Article Title: quickBAM: a parallelized BAM file access API for high-throughput sequence analysis informatics

doi: 10.1093/bioinformatics/btad463

Figure Lengend Snippet: Performance benchmark results of reimplemented flagstats versus stock version. (A) Results using the GIAB HG002 Illumina 2x250 BAM file with an NVMe SSD array available on AWS. (B) Results using the rapid autopsy Bn2 sample BAM file with an NVMe SSD array available on AWS. (C) Results using the GIAB HG002 Illumina 2x250 BAM file with a Lustre distributed file system. (D) Results using the rapid autopsy Bn2 sample BAM file with a Lustre distributed file system.

Article Snippet: GIAB Ashkenazim Trio HG002 and HG004 Illumina 2x250bp novoalign GRCh38 BAM files are available at The rapid autopsy tumor normal sample dataset was from a published study ( ).

Techniques:

Performance benchmark results of reimplemented snp-pileup versus stock version. Note that the stock implementation of snp-pileup does not support multi-threading. (A) Results using the GIAB HG002 and HG004 Illumina 2x250 BAM files with an NVMe SSD array available on AWS. (B) Results using the rapid autopsy Bn2 and Germ1 BAM files with an NVMe SSD array available on AWS. (C) Results using the GIAB HG002 and HG004 Illumina 2x250 BAM file with a Lustre distributed file system. (D) Results using the rapid autopsy Bn2 and Germ1 BAM file with a Lustre distributed file system.

Journal: Bioinformatics

Article Title: quickBAM: a parallelized BAM file access API for high-throughput sequence analysis informatics

doi: 10.1093/bioinformatics/btad463

Figure Lengend Snippet: Performance benchmark results of reimplemented snp-pileup versus stock version. Note that the stock implementation of snp-pileup does not support multi-threading. (A) Results using the GIAB HG002 and HG004 Illumina 2x250 BAM files with an NVMe SSD array available on AWS. (B) Results using the rapid autopsy Bn2 and Germ1 BAM files with an NVMe SSD array available on AWS. (C) Results using the GIAB HG002 and HG004 Illumina 2x250 BAM file with a Lustre distributed file system. (D) Results using the rapid autopsy Bn2 and Germ1 BAM file with a Lustre distributed file system.

Article Snippet: GIAB Ashkenazim Trio HG002 and HG004 Illumina 2x250bp novoalign GRCh38 BAM files are available at The rapid autopsy tumor normal sample dataset was from a published study ( ).

Techniques: