Combined high-depth Illumina+PacBio Sequencing of several samples from FDA-ARGOS

The (real) sequencing data is compiled from a concatenation of sequencing runs from Database for Reference Grade Microbial Sequences (FDA-ARGOS). Specifically, the following samples were sequenced with both Illumina and PacBio. The sample accessions are shown below.

   BioSample    Run        Platform    Organism                                         bases source                                   
   <chr>        <chr>      <chr>       <chr>                                            <dbl> <chr>                                    
 1 SAMN06173354 SRR5409204 ILLUMINA    Bacillus anthracis                          1778000000 Colorado Serum Co., Anthrax Spore Vaccine
 2 SAMN06173354 SRR5409205 PACBIO_SMRT Bacillus anthracis                          2420000000 Colorado Serum Co., Anthrax Spore Vaccine
 3 SAMN06173356 SRR5448657 ILLUMINA    Bacillus circulans                          2311000000 swab with brown-gray powder              
 4 SAMN06173356 SRR5448656 PACBIO_SMRT Bacillus circulans                           242000000 swab with brown-gray powder              
 5 SAMN04875535 SRR4123920 ILLUMINA    Elizabethkingia anophelis                   1357000000 blood                                    
 6 SAMN04875535 SRR4123919 PACBIO_SMRT Elizabethkingia anophelis                   2173000000 blood                                    
 7 SAMN06173306 SRR5413253 ILLUMINA    Escherichia coli O157                       3051000000 clinical isolate                         
 8 SAMN06173306 SRR5413252 PACBIO_SMRT Escherichia coli O157                        915000000 clinical isolate                         
 9 SAMN06173318 SRR5413272 ILLUMINA    Mycobacterium avium subsp. paratuberculosis 1032000000 feces                                    
10 SAMN06173318 SRR5413271 PACBIO_SMRT Mycobacterium avium subsp. paratuberculosis  462000000 feces                                    
11 SAMN07312468 SRR5879398 ILLUMINA    Mycobacterium tuberculosis                  1054000000 human                                    
12 SAMN07312468 SRR5879396 PACBIO_SMRT Mycobacterium tuberculosis                  1854000000 human                                    
13 SAMN04875542 SRR4123931 ILLUMINA    Neisseria gonorrhoeae                       1053000000 ATCC strain                              
14 SAMN04875542 SRR4123930 PACBIO_SMRT Neisseria gonorrhoeae                       1117000000 ATCC strain    

Samples were selected with the SRA Run selector. The SraRunTable.txt file was exported containing the metadata for each sample, and fastq-dump from the SRA toolkit was used to write out fastq files for each run, with paired Illumina data being split into separate _1.fastq.gz and _2.fastq.gz files.