LSC protocols

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LSC specifications

Information


Unique identifier OMICS_05094
Name LSC
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Pacific Biosciences
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Wing Hung Wong <>

Publication for LSC

LSC in pipelines

 (2)
2017
PMCID: 5553090
PMID: 28868132
DOI: 10.5256/f1000research.11392.r19894

[…] in the end of first paragraph, right column, page 10, the word “corrected”/”correction” means the sequencing long reads that are corrected by short reads using error-correction software (e.g., lsc). we have added some annotation for table 2 for better understanding. , ht (3c):  a similar statement is true for figure 5 and the corresponding text (“when using long reads only”): […]

2016
PMCID: 4931320
PMID: 27356984
DOI: 10.1038/ncomms12065

[…] we further aligned them to the grch38 reference genome using the gmap algorithm. to improve iso-seq read alignment, we further performed error correction of all original iso-seq reads using lsc, following similar steps in its original publication. lsc is an algorithm designed for improving pacbio long-read accuracy by short-read alignment from illumina rna-seq. alignment and analysis […]


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LSC in publications

 (12)
PMCID: 5793194
PMID: 29346292
DOI: 10.3390/genes9010043

[…] junction of iso-seq isoforms is also improved with hiseq short reads []. in this case, certain programs have recently been developed such as pacbiotoca (error correction via celera assembler) [], lsc [], lordec [], and proovread []. pacbio long reads for phage, prokaryotic, and eukaryotic genome sequencing are corrected to 99.9% accuracy by pacbiotoca []. the computation method of lsc applies […]

PMCID: 5664107
PMID: 28981454
DOI: 10.3390/genes8100257

[…] each read trimmed. adapters among short-read libraries were then removed using the software cutadapt [], and errors in pacbio long reads were corrected with short-read alignment using the software lsc 1.beta []. following error correction, long and short reads were aligned to the genome using the software hisat [], before being input into the software idp 0.1.9 [] for the detection […]

PMCID: 5498581
PMID: 28680106
DOI: 10.1038/s41467-017-00050-4

[…] reconstruction, long tgs reads usually have a relatively high error rate that hinders their direct application for rna-seq analysis. several tools aim to reduce these error rates including lsc, proovread, lordec, and pbcr, . here we analysed the hybrid long-read error correction tools lsc and lordec., lsc was ~100× slower than lordec (supplementary table ). using lsc and lordec on mcf7 […]

PMCID: 5423905
PMID: 28539927
DOI: 10.3389/fpls.2017.00694

[…] reads from the same study together with pacbio long reads () were quality trimmed and in silico normalized with trinity, and then used to error correct pacbio long reads using three iterations of lsc 1.alpha (). corrected pacbio reads longer than 500 bp and aligned to b73 refgen_v2 along ≥90% of their length with ≥95% identity in pasa were compared to transcripts assembled from rna-seq short […]

PMCID: 4931320
PMID: 27356984
DOI: 10.1038/ncomms12065

[…] we further aligned them to the grch38 reference genome using the gmap algorithm. to improve iso-seq read alignment, we further performed error correction of all original iso-seq reads using lsc, following similar steps in its original publication. lsc is an algorithm designed for improving pacbio long-read accuracy by short-read alignment from illumina rna-seq. alignment and analysis […]


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LSC institution(s)
Department of Statistics, Stanford University, Stanford, CA, USA; Pacific Biosciences of California, Menlo Park, CA, USA
LSC funding source(s)
This work was supported by the National Institutes of Health [R01HG005717 and R01HD057970].

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