LifeScope specifications

Information


Unique identifier OMICS_00667
Name LifeScope
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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LifeScope citations

 (7)
2018
PMCID: 5830406

[…] 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

[…] 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 […]

2016
PMCID: 5269692

[…] technologies) and incubated for 1 hour at 37°c. then, the beads were sequenced using a 5500xl solid system (life technologies)., short reads were mapped to the human reference genome hg19 using lifescope software (life technologies). the resultant bam files were processed with indelrealigner and baserecalibrator tools, followed by identification of single‐nucleotide variants (snv) and small […]

2016
PMCID: 4987512

[…] 5500xl platform (life technologies). mean percentage of coverage ≥5 × was 94.3% with an average depth of coverage of × 60.2., mapping and variant calling of exome sequence reads were performed on lifescope genome analysis software (life technologies) using the genome reference consortium human reference sequence (grch37) as reference. the output gff3 files were annotated using wannovar34. […]

2016
PMCID: 5113843

[…] generate bead templates for solid platform sequencing. samples were sequenced on the 5500xl solid platform (lifetechnologies). the 75-bp sequences produced were mapped in color space using the solid lifescope software version 2.5 (life technologies/invitrogen) using the default parameters against the reference genome set of 2 302 715 separate gene fasta entries. corresponding gtf files […]

LifeScope institution(s)
ThermoFisher

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