BaseSpace protocols

BaseSpace specifications


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

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 [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 […]

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

[…] 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 [38] with allowed mismatches set to 14. […]

PMCID: 5305113
PMID: 28192534
DOI: 10.1371/journal.pone.0171677

[…] heat maps were generated using gene-e (broad institute,, sequencing run data containing base call information was stored and demultiplexed in basespace® sequence hub. the resulting fast.gz files were decompressed using 7-zip to obtain fastq files for read 1 and read 2 for each sample. raw reads quality assessment was performed by qc […]

PMCID: 5499558
PMID: 28549188
DOI: 10.1093/nar/gkx479

[…] bound libraries were pcr-amplified (18 cycles), pooled and size-selected (300–500 nt). samples were sequenced using a nextseq500 to produce single-end 75 reads, and were demultiplexed using illumina basespace servers., for each read we trimmed the first 8 nt (umi, unique molecular identifier) and aligned the rest to the s. cerevisiae genome (version r64-1-1) using hisat2 with default parameters […]

PMCID: 5501799
PMID: 28687745
DOI: 10.1038/s41598-017-04743-0

[…] 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 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 […]

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