LifeScope protocols

LifeScope specifications

Information


Unique identifier OMICS_00667
Name LifeScope
Alternative names LifeScopeTM, LifeScope Genomic Analysis Software
Software type Application/Script, Pipeline/Workflow
Interface Command line interface, Graphical user interface
Restrictions to use None
Input format XSQ
Output format BAM, GFF3
Operating system Unix/Linux
License Commercial
Computer skills Advanced
Version 2.5.1
Stability Stable
Maintained Yes

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Documentation


LifeScope IN pipelines

 (19)
2018
PMCID: 5830406
PMID: 29491376
DOI: 10.1038/s41467-018-03265-1

[…] and transcript annotation from gencode version 19 (equivalent ensembl grch37)57 was used for processing rna-sequencing samples. color space reads from solid sequencing platform were aligned using lifescope, and hisat58 aligner was used for reads from illumina sequencing platform. the reads for gencode transcripts were quantified using htseq-count59 with ‘intersection-strict’ mode., […]

2017
PMCID: 5367703
PMID: 28346506
DOI: 10.1371/journal.pone.0174124

[…] rna-seq kit based on manufacturer’s protocol and sequenced on the life technologies solid 4/5500 system (paired-end: 50x35bp and 75x35bp). reads were aligned to the human genome (hg19) using the lifescope genomic analysis software (applied biosystems; whole transcriptome analysis pipeline, default parameters). expression levels by gene were determined with the htseq-count software [46] using […]

2017
PMCID: 5727439
PMID: 29244185
DOI: 10.1093/nar/gkx896

[…] analysis kit (thermo fisher scientific). pooled barcoded libraries were sequenced to generate paired-end 35 × 75 bp reads and colorspace xsq data was aligned to mouse genome version mm9 using lifescope software (thermo fisher scientific)., gene-wise read counts were analyzed for differential expression using deseq2 (34). when comparing wild type myoblasts and myotubes, we used a linear […]

2016
PMCID: 4761217
PMID: 26896187
DOI: 10.1186/s12863-016-0354-9

[…] of medicine, vilnius university with the use of a 5500 solid™ sequencer according to the optimised manufacturer’s protocols. sequence alignment and secondary and tertiary analysis performed using lifescope™ genomic analysis software v2.5. the genome analysis toolkit’s (gatk) combinevariants tool [18, 19] was used to combine all identified genomic variants from 98 individuals into single vcf […]

2016
PMCID: 4824866
PMID: 26785728
DOI: 10.1074/mcp.M115.054122

[…] a solid 6-lane flowchip for 1 h at 37 °c. the dna on the flowchip was sequenced in read length of 75 bases in a 5500xl solid system., procession and read mapping of the run was carried out with the lifescope software analysis tool (life technologies) and reference genome grch37/hg19. statistical analysis was performed with r (25). normalization and differential expression calculations […]

LifeScope institution(s)
ThermoFisher

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