smrt pipeline protocols

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smrt pipeline specifications

Information


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

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Maintainer


  • person_outline Denye Ogeh <>

Publication for smrt pipeline

smrt pipeline in pipeline

2017
PMCID: 5798397
PMID: 28720171
DOI: 10.1017/S0031182017001329

[…] 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 […]


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smrt pipeline in publications

 (9)
PMCID: 5920184
PMID: 29700149
DOI: 10.1128/genomeA.00311-18

[…] the two b. leptomitoformis strains., modified bases are in bold, and modified bases on an opposite strand are in bold and underlined., the s.ble401orfep modified motif was not detected directly by smrt pipeline motif and modification software in b. leptomitoformis strain d-401, but it was confirmed manually using pbmotstat software (t.v.)., nd, not determined., the complete, closed genome […]

PMCID: 5876484
PMID: 29599160
DOI: 10.1128/genomeA.00201-18

[…] 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, […]

PMCID: 5816337
PMID: 29483921
DOI: 10.3389/fpls.2018.00005

[…] 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 […]

PMCID: 5798397
PMID: 28720171
DOI: 10.1017/S0031182017001329

[…] 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 […]

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

[…] 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 […]


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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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