BaseSpace statistics

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Citations per year

Number of citations per year for the bioinformatics software tool BaseSpace

Tool usage distribution map

This map represents all the scientific publications referring to BaseSpace per scientific context
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Associated diseases

This word cloud represents BaseSpace usage per disease context

Popular tool citations

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


FACS Seq analysis of Pax3 derived cells identifies non myogenic lineages in the embryonic forelimb

Sci Rep
PMCID: 5956100
PMID: 29769607
DOI: 10.1038/s41598-018-25998-1
call_split See protocol

[…] d, corresponding to six (E11.5), seven (E12.5), nine (E13.5), and six (E14.5) biological replicates. Primary Illumina data image analysis, base calling, and read-quality filtering were done using the Casava pipeline version 1.8.2 (Illumina). Each sample was processed and analyzed with the same methods. After filtering low quality reads TopHat version 2.1.0 was used to align all reads to the mm10 g […]


Case Report: Identification of an HNF1B p.Arg527Gln mutation in a Maltese patient with atypical early onset diabetes and diabetic nephropathy

PMCID: 5952643
PMID: 29764441
DOI: 10.1186/s12902-018-0257-z
call_split See protocol

[…] Image analysis was performed with the default parameters of Illumina RTA pipeline, and base calling was carried out using CASAVA. The sequence reads were mapped and aligned to the Human Reference Genome (UCSC hg19, NCBI build 37) using the Burrows-Wheeler transformation algorithm, and duplicated reads were removed using […]


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

[…] CA, 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. Differentially […]


Additional oxidative stress reroutes the global response of Aspergillus fumigatus to iron depletion

BMC Genomics
PMCID: 5946477
PMID: 29747589
DOI: 10.1186/s12864-018-4730-x

[…] formed on an Illumina HiScan SQ instrument (Illumina, San Diego, CA, USA). Each library pool was sequenced in one lane of a sequencing flow cell, and 16–18 million reads per sample were obtained. The CASAVA software was used for pass filtering and demultiplexing processing.Reads were aligned to A fumigatus (Af293) genome (Genome: A_fumigatus_Af293_version_s03-m05-r04_chromosomes.fasta.gz;  http:// […]


Transcriptome and Co Expression Network Analyses Identify Key Genes Regulating Nitrogen Use Efficiency in Brassica juncea L.

Sci Rep
PMCID: 5945678
PMID: 29748645
DOI: 10.1038/s41598-018-25826-6

[…] Paired-end (PE) read sequences of length 72 bp each with an insert-length of 260 bp were generated using CASAVA package. Quality assessment of read sequences was performed using read quality filtering tool, filteR in which poor quality reads and adapter contaminated reads were filtered-out. De novo assem […]


NOTCH signaling specifies arterial type definitive hemogenic endothelium from human pluripotent stem cells

Nat Commun
PMCID: 5940870
PMID: 29739946
DOI: 10.1038/s41467-018-04134-7

[…] encing was performed using the HiSeq 3000 (Illumina, San Diego, CA) with a single read of 64 bp and index read of 7 bp.Base-calling and demultiplexing were completed with the Illumina Genome Analyzer Casava Software, version 1.8.2. Following quality assessment and filtering for adapter molecules and other sequencing artifacts, the remaining sequencing reads were aligned to transcript sequences cor […]

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BaseSpace institution(s)
Illumina, San Diego, CA, USA

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