READSCAN protocols

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READSCAN specifications

Information


Unique identifier OMICS_00222
Name READSCAN
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained No

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Publication for READSCAN

READSCAN in pipeline

2017
PMCID: 5642267
PMID: 28855268
DOI: 10.1530/EJE-17-0277

[…] subjected to the same analysis and employed as negative controls to detect technical false positives. as a complement, all generated sequence data were analyzed using the pathogen discovery software readscan (). this method has previously been utilized by tang et al. (), who successfully identified 28 different known viruses and a novel enterovirus strain among 4433 tumor transcriptomes from 19 […]


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READSCAN in publications

 (4)
PMCID: 5924777
PMID: 29740407
DOI: 10.3389/fmicb.2018.00749

[…] ensembleassembler, facs, kraken, lmat, metavir, metlab, smart, taxonomer and virana), or hours (19 workflows: giant virus finder, gottcha, imsa, megan, mepic, metashot, metavir 2, nbc, provide, readscan, rega typing tool, riems, rins, slim, surpi, taxy-pro, “unknown pathogens from mixed clinical samples,” vip and viromescan), or even days (5 workflows: exhaustive iterative assembly, […]

PMCID: 5642267
PMID: 28855268
DOI: 10.1530/EJE-17-0277

[…] subjected to the same analysis and employed as negative controls to detect technical false positives. as a complement, all generated sequence data were analyzed using the pathogen discovery software readscan (). this method has previously been utilized by tang et al. (), who successfully identified 28 different known viruses and a novel enterovirus strain among 4433 tumor transcriptomes from 19 […]

PMCID: 4677295
PMID: 26658849
DOI: 10.1038/srep18081

[…] other reports (). we next analyzed the five breast cancer rnaseq datasets (), sequenced to an average of 40 million sequencing reads per sample, using three different bioinformatic pipelines: rins, readscan and virusfinder 2.0. in no instance did we find any evidence of hpv, or other viral transcripts, in the samples that were positive for hpv dna., it is known that there are geographical […]

PMCID: 5964995
PMID: 23725672
DOI: 10.1016/j.mib.2013.05.001

[…] protein sequences using methods such as hmmer [,]. dedicated bioinformatics analysis pipelines, such as pathseq, used to detect fusobacterium bacteria in colon cancer tissues [], rins, capsid, and readscan are now available for automated pathogen identification from ngs data [–], although their performance has yet to be rigorously tested on a large number of clinical samples. ongoing […]


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READSCAN institution(s)
Pathogen Genomics Laboratory, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia

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