BaseSpace protocols

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BaseSpace specifications

Information


Unique identifier OMICS_01213
Name BaseSpace
Alternative name CASAVA (Consensus assessment of sequence and variation)
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 in pipelines

 (60)
2018
PMCID: 5839370
PMID: 29515789
DOI: 10.18632/oncotarget.24273

[…] a nextseq 500 sequencer (illumina, san diego, ca) using a 2 × 150 paired-end sequencing strategy., primary basecall sequencing outputs were converted to fastq format and demultiplexed on illumina’s basespace. read trimming and alignment were performed with nextgene software (softgenetics, state college, pa). reads with median base phred33 quality score ≥ 10, ≤ 3 uncalled bases, ≥ 20 total bases […]

2018
PMCID: 5903673
PMID: 29621242
DOI: 10.1371/journal.pgen.1007308

[…] 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 []., 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 of na12878 […]

2018
PMCID: 5911478
PMID: 29713312
DOI: 10.3389/fendo.2018.00158

[…] using pi bc v2 chip on ion proton system (all from life technologies, usa). two to three mrna libraries were pooled into a single chip., preprocessing of mirna sequencing data was executed in basespace software (illumina, usa), and fastq files were generated. mirna analysis app version 1.0.0 was used for determination of differentially expressed (de) mirnas using the workflow described […]

2018
PMCID: 5932385
PMID: 29755449
DOI: 10.3389/fimmu.2018.00638

[…] reads per sample using 75 base pair paired-end reads for a total output of ~18 gb. the raw image files from the nextseq sequencer were de-multiplexed and converted to fastq files using the bcl2fastq basespace app (illumina). rna-seq analysis was performed on the existing annotated reference transcriptome (mouse) – no alternate transcript discovery was performed. adapter sequences and low-quality […]

2018
PMCID: 5935984
PMID: 29728062
DOI: 10.1186/s12864-018-4677-y

[…] using qiagen (germantown, md) clc genomics workbench 8.5.1 for mapping trimmed reads to the ensemble grch38.82 noncoding rna database and quantifying the levels of small rna expression., illumina basespace 16s metagenomics app was used to generate a classification of reads at taxonomic levels from kingdom to species. the classification step uses a proprietary algorithm that provides […]


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BaseSpace in publications

 (192)
PMCID: 5935984
PMID: 29728062
DOI: 10.1186/s12864-018-4677-y

[…] 16s rrna gene sequencing showed that similar numbers of reads were generated from the illumina protocol (2,249,926) and the sub-nanomolar protocol (2,148,506). sunburst charts created using illumina basespace 16s metagenomics app (fig. ) illustrate the highly similar taxonomic hierarchy and relative abundance of classification. additional file : table s7 (figure and data) further demonstrates […]

PMCID: 5932012
PMID: 29720585
DOI: 10.1038/s41467-018-04180-1

[…] and 2 × 150 bp paired-end sequencing was performed using the illumina nextseq 500 (illumina). paired-end reads from the targeted amplicon deep sequencing were aligned to the mouse genome mm9 on basespace (illumina) using a banded smith–waterman algorithm and bedtools was used to calculate coverage. mpileup files were created using samtools (1.3.1) and variant calling was performed using […]

PMCID: 5930336
PMID: 29475863
DOI: 10.1128/AEM.02156-17

[…] was initiated using the fluidigm sequencing primers targeting the gene-specific primer and common sequence tag regions. demultiplexing of reads was performed on the miseq instrument using illumina basespace. sequencing was performed at the w. m. keck center for comparative and functional genomics at the university of illinois at urbana-champaign (uiuc)., sequence reads from vibrio species 16s […]

PMCID: 5911478
PMID: 29713312
DOI: 10.3389/fendo.2018.00158

[…] using pi bc v2 chip on ion proton system (all from life technologies, usa). two to three mrna libraries were pooled into a single chip., preprocessing of mirna sequencing data was executed in basespace software (illumina, usa), and fastq files were generated. mirna analysis app version 1.0.0 was used for determination of differentially expressed (de) mirnas using the workflow described […]

PMCID: 5897794
PMID: 29650585
DOI: 10.1128/genomeA.00332-18

[…] kit) before multiplex pooling and sequencing in a 2 × 300-bp paired-end (pe) flow cell on the miseq platform (illumina). adapters were computationally segregated and trimmed in the illumina basespace pipeline and then partially assembled using the velvet assembly tool (). the chromobacterium sp. nov. mwu13-2610 genome has 62.4% gc content and consists of 4,387,023 bp distributed […]


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