Open brooksph opened 6 years ago
One exclusively short read and one hybrid
If it's helpful, the simulated "frankengenome" dataset has a crazy mix of short bacterial, archaeal, viral, and eukaryotic reads: https://ftp-private.ncbi.nlm.nih.gov/nist-immsa/IMMSA/UnAmbiguouslyMapped_ds.frankengenome.fq.gz
I attached a truth file for it that follows the same format as the other unambiguously mapped datasets in the McIntyre et al. 2017 study: UnAmbiguouslyMapped_ds_frankengenome_TRUTH.txt
Column 1 = NCBI Taxonomy ID Column 2 = Number of reads simulated from that organism Column 3 = Abundance of that organism in the dataset Column 4 = Rank Column 5 = Species name
The frankengenome won't be a good resource for generating spike-in datasets, but it's an additional dataset option if you'd like to do more testing with reads from viruses and eukaryotes.
Expected behavior
These data were identified by Nicolete (SigSci) Updates from Nicolette - https://docs.google.com/document/d/1uYqs939MU55D_3La8RUc8NJIYVrjLmVD-q_Tw5_Bjbg/edit
Viral DNA spike-ins (non-assembled datasets): Organism: Human betaherpesvirus 5 (dsDNA) Technology: Illumina Genome Analyzer II https://www.ncbi.nlm.nih.gov/sra/ERX004415[accn] Technology: Illumina HiSeq 2000 https://www.ncbi.nlm.nih.gov/sra/ERX2083171[accn]
Organism: Human gammaherpesvirus 4 (dsDNA) (alternate name: Epstein-Barr virus) Technology: Illumina HiSeq 2000 https://www.ncbi.nlm.nih.gov/sra/ERX218636[accn] Organism: Vaccinia virus (dsDNA) Technology: Illumina HiSeq 2000 https://www.ncbi.nlm.nih.gov/sra/SRX2421177[accn] Organism: Cowpox virus (dsDNA) Technology: Illumina MiSeq https://www.ncbi.nlm.nih.gov/sra/SRX3106169[accn] Organism: Torque teno virus (ssDNA) Technology: Illumina HiSeq 4000 https://www.ncbi.nlm.nih.gov/sra/SRX1762570[accn] Organism: Adeno-associated virus (ssDNA) Technology: Illumina HiSeq 2500 https://www.ncbi.nlm.nih.gov/sra/SRX1960902[accn] Organism: Human bocavirus 1 (ssDNA) Technology: Illumina HiSeq 2500 https://www.ncbi.nlm.nih.gov/sra/ERX1470610[accn] Organism: Enterobacteria phage T7 Technology: Illumina HiSeq 2500 https://www.ncbi.nlm.nih.gov/sra/SRX2365806[accn] Organism: Enterobacteria phage T3 Technology: Illumina HiSeq 2000 https://www.ncbi.nlm.nih.gov/sra/SRX209596[accn] Organism: Bacillus phage BC01 Technology: Illumina HiSeq 4000 https://www.ncbi.nlm.nih.gov/sra/SRX3214803[accn] Eukaryotic microbe spike-ins: Organism: Saccharomyces cerevisiae Y12 Illumina HiSeq 4000 https://www.ncbi.nlm.nih.gov/sra/SRX2487940[accn] PacBio RS II https://www.ncbi.nlm.nih.gov/sra/SRX2485790[accn] Organism: Schizosaccharomyces kambucha strain:SZY13 Illumina HiSeq 2000 https://www.ncbi.nlm.nih.gov/sra/SRX521792[accn] PacBio RS https://www.ncbi.nlm.nih.gov/sra/SRX521793[accn] Organism: Colletotrichum higginsianum IMI 349063 Illumina HiSeq 1500 https://www.ncbi.nlm.nih.gov/sra/SRX2765599[accn] PacBio RS II https://www.ncbi.nlm.nih.gov/sra/SRX1567884[accn] Organism: [Candida] auris Illumina HiSeq 2500 https://www.ncbi.nlm.nih.gov/sra/SRX1939498[accn] PacBio RS II https://www.ncbi.nlm.nih.gov/sra/SRX1939493[accn] Organism: Fusarium poae isolate 2516 Illumina HiSeq 2000 https://www.ncbi.nlm.nih.gov/sra/SRX1977327[accn] PacBio RS II https://www.ncbi.nlm.nih.gov/sra/SRX1977328[accn]
Actual behavior
Steps to reproduce the behavior