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smrt pipeline specifications


Unique identifier OMICS_14376
Name smrt pipeline
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes




No version available



  • person_outline Denye Ogeh

Publication for smrt pipeline

smrt pipeline citations


Whole Genome Sequence of Acetobacter orientalis Strain FAN1, Isolated from Caucasian Yogurt

Genome Announc
PMCID: 5876484
PMID: 29599160
DOI: 10.1128/genomeA.00201-18
call_split See protocol

[…] l method () and was subjected to sequencing with PacBio RS II and Illumina HiSeq 2500 systems (Hokkaido System Science Co., Ltd., Sapporo, Japan). The complete genome sequence was assembled using the SMRT Pipeline (HGAP.2) program (), followed by gene annotation using the Glimmer, RNAmmer, tRNAscan-SE, BLAST, and Blast2GO programs ().The FAN1 strain was found to have two circular DNAs, with length […]


Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching

Front Plant Sci
PMCID: 5816337
PMID: 29483921
DOI: 10.3389/fpls.2018.00005

[…] were run once. Initial processing of the raw Iso-Seq sequence data assembly was performed at Arizona Genomics Institute essentially as described. Primary Iso-Seq data analysis was performed using the SMRT pipeline (Version 1.87.139483). Initial alignments of Iso-Seq reads to poplar genome for plotting on GMOD GBrowse were produced using STAR aligner V.2.5.2a (). STAR output files in BAM format wer […]


PacBio assembly of a Plasmodium knowlesi genome sequence with Hi C correction and manual annotation of the SICAvar gene family

PMCID: 5798397
PMID: 28720171
DOI: 10.1017/S0031182017001329
call_split See protocol

[…] inSubReadLength = 500, readScore = 0·80 and minLength = 100. After filtering the reads, HGAP3 de novo assembly was performed using the Georgia Advanced Computing Resource Center, GACRC Sapelo cluster SMRT pipeline. The error-correction module was used to quality control the subreads (defined as minimum subread length of 100 bp, a minimum read quality of 0·80) and the longer reads passing this thre […]


Generality of toxins in defensive symbiosis: Ribosome inactivating proteins and defense against parasitic wasps in Drosophila

PLoS Pathog
PMCID: 5500355
PMID: 28683136
DOI: 10.1371/journal.ppat.1006431

[…] logies (Genome Quebec). We sequenced long reads on three SMRT cells and short reads in 0.4 of a sequencing lane. A preliminary sNeo genome was assembled by Genome Quebec using long reads only via the SMRT Pipeline, with an estimated genome size of 1.8 Mb. The assembly contains Drosophila-derived sequences, decontaminating and error-correcting these data is an ongoing project. We searched for RIP g […]


Clostridium chauvoei, an Evolutionary Dead End Pathogen

Front Microbiol
PMCID: 5465433
PMID: 28649238
DOI: 10.3389/fmicb.2017.01054

[…] cies. The genome of this strain was sequenced using Pacific Biosciences R.S. (PacBio) sequencing (85,000 reads/2950 bp average read length). The reads of the PacBio sequencing were assembled with the SMRT Pipeline HGAP3 into one circularized closed contig. The chromosome sequence of C. chauvoei strain JF4335 is 2,887,451 bp with a G+C content of 28.3% and with a total of 2624 predicted coding sequ […]


Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana)

PMCID: 5144951
PMID: 27799338
DOI: 10.1534/g3.116.032805

[…] early draft genome assembly, contributing to a reduction of the mapping rates.The single PacBio Iso-Seq embryo library (3–6 kb size selected) was selected to analyze each of the four outputs from the SMRT pipeline. After full-length transcripts (Pa in ) were assembled from raw reads, the software provides an optional isoform level clustering step to reduce isoform redundancy (Pb1 in ), and an addi […]


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smrt pipeline institution(s)
Department of Genetics, University of Leicester, Leicester, UK
smrt pipeline funding source(s)
This work has been supported by the Niger Delta Development Commission Postgraduate scholarship scheme.

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