BaseSpace specifications

Information


Unique identifier OMICS_01213
Name BaseSpace
Software type Framework/Library
Interface Command line interface
Restrictions to use License purchase required
Operating system Unix/Linux
Parallelization MapReduce
License Commercial
Computer skills Advanced
Stability Stable
High performance computing Yes
Maintained Yes

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BaseSpace citations

 (11)
2018
PMCID: 5903673

[…] 45x coverage), and illumina paired-end rna reads (srr1153470, srr1258218, err356372; 300 million pe reads). the genotype data for the parents (na12891 and na12892) were obtained from illumina basespace [17]., we generated an in-house genome-wide variant dataset for na12878 using standard bioinformatics methods to benchmark and compare various phasing strategies. the in-house set […]

2017
PMCID: 5708669

[…] the next generation sequencing core at the perelman school of medicine (ngsc, ngsc.med.upenn.edu). sequence data were acquired and processed per ngsc instructions followed by uploading to illumina basespace sequence hub for downstream analysis. sequence reads were aligned to the latest canine reference genome, canfam3. reads with a mapping quality less than 20 were filtered out, unmapped reads […]

2017
PMCID: 5539636

[…] and clustered on illumina truseq v3 flowcell. the clustered flowcell was sequenced on an illumina hiseq 1000 in 100-base single-read reactions. sequenced reads were processed using the illumina basespace cloud environments rnaexpress app workflow version 1.0.0. the reads were aligned to the ucsc (http://genome.ucsc.edu/index.html) rn5 reference assembly using the star aligner [53]. gene […]

2017
PMCID: 5501799

[…] sequenced on the miniseq illumina platform using miniseq high output (300 cycles) sequencing chemistry., primary data analysis was performed using the truseq amplicon workflow (version 2.0.0.0.) via basespace sequence hub. (alignment to hg19 reference genome with samtools isis smith-waterman-gotoh and base calling with somatic variant caller) for primary filtering and annotation of all datasets […]

2017
PMCID: 5335663

[…] platform (illumina) with a 2 × 75 paired-end read length giving 719 million raw reads (average depth 45 million reads per sample). reads were filtered using the fastq toolkit v2.0.0 in the illumina basespace cloud computing environment to remove adapter sequences and reads with phred score <20 or length <20 bp35. filtered reads were checked using fastqc before aligning with star 2.0 […]

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