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SRX173233: Illumina deep sequencing corresponding to human serum sample from an individual infected with BASV rhabdovirus
1 ILLUMINA (Illumina HiSeq 2000) run: 3.1M spots, 621.6M bases, 369.9Mb downloads

Design: To recover additional BASV sequence, two sets of cDNA libraries were prepared from DNase-treated extracted RNA using a random PCR amplification method as described previously [34], or random hexamer priming according to the manufacturer’s protocol (Illumina). The libraries were then pooled and sequenced on two lanes of an Illumina HiSeq 2000. Raw Illumina sequences consisting of 100 base pair (bp) paired-end reads were filtered to exclude low-complexity, homopolymeric, and low-quality sequences. Rapid classification of the ~140 million 100-bp paired-end Illumina reads was performed using a modified cloud computing-based computational analysis pipeline [16] (Veeraraghavan, Sittler, and Chiu, manuscript in preparation). Specifically, the dataset presented here was stripped of human and some bacterial reads by alignments to the human genomic database hg19, human transcriptome RefSeq database, and a bacterial database composed of all Burkholderia sequences in GenBank. Iterative alignments were made using SOAP, BLAT, BLASTn, and finally, a new matching algorithm called SNAP (Zaharia, et al., 2011, arXiv:111.5572).
Submitted by: University of California, San Francisco
Study: Bas-Congo virus Metagenome
show Abstracthide Abstract
Clinical metagenomics of human serum samples. Clinical human samples (with the human reads removed) such as respiratory secretions, diarrhea, and serum were used to isolate reads for endogenous and exogenous viruses, bacteria etc. (nonhuman reads).
Sample: Human serum sample from patient infected with BASV rhabdovirus
SAMN01103168 • SRS353125 • All experiments • All runs
Organism: Hariotina
Library:
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Source: METAGENOMIC
Selection: RANDOM PCR
Layout: PAIRED
Spot descriptor:
forward101  reverse

Pipeline: show...hide...
ProgramVersion
Btrim
Geneious5.3.4
BLAT
SOAP
BLASTn
BLASTx
SNAP
Links:
Runs: 1 run, 3.1M spots, 621.6M bases, 369.9Mb
Run# of Spots# of BasesSizePublished
SRR5339783,108,170621.6M369.9Mb2015-07-22

ID:
224185

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