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SMRT-Analysis specifications


Unique identifier OMICS_05142
Name SMRT-Analysis
Alternative names Single Molecule Real-Time Analysis, smrtanalysis, SMRT Analysis, SMRT
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Biological technology Pacific Biosciences
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes




No version available

SMRT-Analysis citations


Complete Genome Sequence of Staphylococcus haemolyticus Type Strain SGAir0252

Genome Announc
PMCID: 5946035
PMID: 29748397
DOI: 10.1128/genomeA.00229-18
call_split See protocol

[…] eq platform provided 653,569 (121.27-fold coverage) short reads.De novo genome assembly of long reads was performed using the Hierarchical Genome Assembly Process version 3 (HGAP3) implemented in the SMRT analysis algorithm version 2.3.0 (). Different stages of the process involved preassembly, de novo assembly with Celera Assembler, and polishing with Quiver (). Illumina reads were used to improv […]


Complete Genome Sequences of Two Atypical Enteropathogenic Escherichia coli O145 Environmental Strains

Genome Announc
PMCID: 5946043
PMID: 29748413
DOI: 10.1128/genomeA.00418-18
call_split See protocol

[…] SMRT cells were run with a 0.1-nM on-plate concentration, P6/C4 sequencing chemistry, MagBeadOneCellPerWell v1 collection protocol, and 360-min data collection mode. A FASTQ file was generated using SMRT Analysis (v 2.3.0), and assembly was done with RS_HGAP_Assembly.3. The complete genome sequences were submitted to GenBank for annotation using the NCBI Prokaryotic Genome Annotation Pipeline.The […]


Comparative genomics of cocci shaped Sporosarcina strains with diverse spatial isolation

BMC Genomics
PMCID: 5930826
PMID: 29716534
DOI: 10.1186/s12864-018-4635-8

[…] Previously described SMRTanalysis software was used to identify any base modifications by identifying locations of methylation associated with different motifs between all six PacBio sequenced genomes. Additionally, each […]


Identification and pathogenomic analysis of an Escherichia coli strain producing a novel Shiga toxin 2 subtype

Sci Rep
PMCID: 5928088
PMID: 29712985
DOI: 10.1038/s41598-018-25233-x
call_split See protocol

[…] was sequenced by single molecule, real-time (SMRT) technology using the Pacific Biosciences (PacBio) sequencing platform. The data were assembled to generate one circular genome without gaps by using SMRT Analysis 2.3.0. The protein-coding sequences (CDSs), tRNAs and rRNAs were predicted using GeneMarkS. The prophages were predicated by the PHAge Search Tool (PHAST). The virulence factors were pre […]


Complete Genome Sequence of Multiple Antibiotic Resistant Streptococcus parauberis Strain SPOF3K, Isolated from Diseased Olive Flounder (Paralichthys olivaceus)

Genome Announc
PMCID: 5920164
PMID: 29700142
DOI: 10.1128/genomeA.00248-18
call_split See protocol

[…] DNA purification kit (Promega, USA). Whole-genome sequencing was performed with PacBio 20K (Pacific Biosciences) single-molecule real-time (SMRT) technology. Raw sequences were assembled using PacBio SMRT Analysis 2.3.0. Sequencing results yielded a total of 101,064 PacBio reads, with a coverage of 703.34×. Two gapless contigs (2,128,740 bp and 23,538 bp) were obtained after sequence assembly. Gen […]


Complete Genome Sequence of a VIM 1 Producing Salmonella enterica subsp. enterica Serovar Infantis Isolate Derived from Minced Pork Meat

Genome Announc
PMCID: 5920186
PMID: 29700156
DOI: 10.1128/genomeA.00327-18
call_split See protocol

[…] A de novo genome assembly was performed based on 32,727 reads from one single-molecule real-time (SMRT) cell (mean read length, 12,946 bp; N50 read length, 17,965 bp; mean read score, 0.85) using the SMRT Analysis software (version 2.3.0; Pacific Biosciences, USA) and resulted in two contigs with an average coverage of 75.27 per consensus base. Illumina paired-end short-read data were mapped again […]


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