BCL2FASTQ Conversion Software statistics

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Citations per year

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Popular tool citations

chevron_left Demultiplexing File format conversion Adapter trimming Base calling chevron_right
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Associated diseases

Associated diseases


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BCL2FASTQ Conversion Software specifications


Unique identifier OMICS_07545
Name BCL2FASTQ Conversion Software
Alternative names bcl2fastq2, bcl2fastq, bcltofastq
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input format BCL
Output format FASTQ
Biological technology Illumina
Operating system Unix/Linux
Computer skills Advanced
Version 2.20
Stability Stable
Maintained Yes



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  • person_outline omiRas Team <>

BCL2FASTQ Conversion Software in pipelines

PMCID: 5754119
PMID: 29300782
DOI: 10.1371/journal.ppat.1006750

[…] generated 2,844,500 clusters (5,689,000 raw reads) on an illumina hiseq 1500 at the farncombe metagenomics facility (mcmaster university, hamilton ontario, canada)., reads were demultiplexed using casava-1.8.2 (illumina, san diego, california), then adapters were trimmed and reads merged using leehom [] with adna specific settings (—ancientdna). these processed reads were mapped […]

PMCID: 5756339
PMID: 29304863
DOI: 10.1186/s12931-017-0708-5

[…] truseq sr v3 flow cells on an illumina hiseq 2500 (illumina) and run for 50 cycles using a single-read recipe (truseq sbs kit v3, illumina) according to the manufacturer’s instructions. illumina casava pipeline (released version 1.8, illumina) was used to obtain de-multiplexed sequencing reads (fastq files) passed the default purify filter. additional quality filtering used fastx-toolkit […]

PMCID: 5758812
PMID: 29311649
DOI: 10.1038/s41598-017-17878-x

[…] 1 (hprt), respectively. primer sequences are described in table . library prep for ngs, following [46] and sequencing performed on illumina 2500 at 50 bp single read. fasta files created (illumina casava-1.8.2 software) and mapped (tophat2 version v2.0.10) against the mouse genome, build mm9. approximately, 85–90% mapping rate was observed. only uniquely mapped reads determined the number […]

PMCID: 5762668
PMID: 29321689
DOI: 10.1038/s41598-017-18675-2

[…] buffer. after 50 cycles using a single-read recipe (truseq sbs kit v3, illumina), de-multiplexed sequencing reads (fastq files) that passed the default purify filter were obtained using the illumina casava pipeline (version 1.8)., to analyze the rna-seq data from human smcs and ecs, we used hg19 (human genome version 19, ucsc) as the human reference genome. a bowtie 2 index was built, […]

PMCID: 5764939
PMID: 29326215
DOI: 10.1128/genomeA.01430-17

[…] 8.0 pm dna, standard illumina primers, and hiseq control software hcs v2.2.58. image analysis, base calling, and quality check were performed with the illumina data analysis pipeline rta v1.18.64 and bcl2fastq v1.8.4. reads were trimmed for adapter sequences and filtered for sequence quality using the in-house tool fastqfilter v2.05. the short-read genome assembler abyss v1.3.7 () was used for ass […]

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BCL2FASTQ Conversion Software in publications

PMCID: 5958073
PMID: 29773913
DOI: 10.1038/s41598-018-25963-y

[…] (illumina, san diego, ca, usa) and were sequenced by nextseq 500 (illumina) in the single-end mode. three biological replicates were analyzed. the produced bcl files were converted to fastq files by bcl2fastq (illumina). the reads were analyzed as previously described and were mapped to the arabidopsis reference (tair10) by bowtie 1.2.1 with the following parameters: ‘-all -best -strata’ (table ) […]

PMCID: 5956100
PMID: 29769607
DOI: 10.1038/s41598-018-25998-1

[…] 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 […]

PMCID: 5952841
PMID: 29759062
DOI: 10.1186/s12974-018-1166-9

[…] stranded mrna neoprep kits (illumina) and sequenced on a nextseq 500 (illumina) at a read depth of 10–20 million reads per sample (75 base pair single-end reads). fastq files were assembled using bcl2fastq., sequence reads were aligned to mouse genome mm10/grcm38 assembly using star 2.5.2a (http://github.com/alexdobin/star; parameters: --outfiltermultimapnmax 20 --outfiltertype bysjout […]

PMCID: 5951918
PMID: 29760424
DOI: 10.1038/s41467-018-04215-7

[…] converted to illumina-compatible ngs libraries and sequencing was done using the miseq (illumina) with the 600 bp v3 reagents kit following the manufacturers instructions. using illumina’s pipeline (bcl2fastq.2.17.4) the fastq files for the individual samples were generated., dna methylation analysis: data was cleaned from adaptor sequences and a minimum of a read length (50) and base quality […]

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

[…] illumina gaiix were submitted as bioproject prjna383771 to the ncbi sequence read archive., 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 […]

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