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chevron_left Prognostic biomarker identification Read alignment SNP detection Haplotype association SNV detection Metagenomic data visualization Gene set enrichment analysis File format conversion Transcription factor binding site prediction Homology-based taxonomic classification Prediction-Based Taxonomic Microbial strain identification De novo motif discovery Plasmid detection Multilocus sequence typing Indel detection Base calling Virulence gene detection chevron_right

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BaseSpace specifications


Unique identifier OMICS_01213
Name BaseSpace
Alternative names Consensus assessment of sequence and variation, CASAVA
Software type Framework/Library
Interface Command line interface
Restrictions to use License purchase required
Biological technology Illumina
Operating system Unix/Linux
Parallelization MapReduce
License Commercial
Computer skills Advanced
Stability Stable
High performance computing Yes
Registration required Yes
Maintained Yes


  • 16S Metagenomics
  • Amplicon DS
  • Bacterial Analysis Pipeline
  • Cancer Variant Caller
  • ChiPSeq
  • DNA Amplicon app
  • E. coli Serotyping App
  • Enrichment
  • GENIUS Metagenomics
  • Benchmarking
  • ITS Metagenomics
  • Melanome Profiler


No version available

BaseSpace citations


Transcriptome analysis of alcohol treated microglia reveals downregulation of beta amyloid phagocytosis

PMCID: 5952855
PMID: 29759078
DOI: 10.1186/s12974-018-1184-7
call_split See protocol

[…] usa) producing about 500 m reads of non-paired 75-nt sequence. up to 32 barcoded samples were pooled together producing on average 12 m reads per sample. rnaseq analysis was carried out using the basespace platform from illumina. the rnaseq-generated fastq files were aligned to the uscsrn5 rattus norvegicus reference genome with star aligner [] with allowed mismatches set to 14. […]


Robust Sub nanomolar Library Preparation for High Throughput Next Generation Sequencing

BMC Genomics
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 […]


De novo activating mutations drive clonal evolution and enhance clonal fitness in KMT2A rearranged leukemia

Nat Commun
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 […]


Environmental Controls of Oyster Pathogenic Vibrio spp. in Oregon Estuaries and a Shellfish Hatchery

Appl Environ Microbiol
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 […]


Immunization Elicits Antigen Specific Antibody Sequestration in Dorsal Root Ganglia Sensory Neurons

Front Immunol
PMCID: 5932385
PMID: 29755449
DOI: 10.3389/fimmu.2018.00638
call_split See protocol

[…] 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 […]


Integrated Characterization of MicroRNA and mRNA Transcriptome in Papillary Thyroid Carcinoma

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 […]

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