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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




No version available



  • person_outline omiRas Team

BCL2FASTQ Conversion Software citations


Auxin decreases chromatin accessibility through the TIR1/AFBs auxin signaling pathway in proliferative cells

Sci Rep
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 ) […]


Parental haplotype specific single cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells

Nat Commun
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 (15) […]


Circular RNA expression and regulatory network prediction in posterior cingulate astrocytes in elderly subjects

BMC Genomics
PMCID: 5941680
PMID: 29739336
DOI: 10.1186/s12864-018-4670-5

[…] The data analysis workflow is summarized in Additional file : Figure S3. Raw sequencing data, in the form of basecall files (BCLs), were converted to FASTQ format using Illumina’s bcl2fastq conversion software and quality checked using FastQC []. To eliminate variance in circRNA detection that could arise due to differences in the number of sequencing reads, all FASTQ files wer […]


Time resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

BMC Biol
PMCID: 5937035
PMID: 29730990
DOI: 10.1186/s12915-018-0518-3

[…] average, 18.9 million read pairs were obtained per sample (mean ± SD 18.9 × 106 ± 5.23 × 106; range 5.3 × 106 to 32.1 × 106). BCL basecall files were de-multiplexed and converted to FASTQ files with bcl2fastq v1.8.4. […]


Evaluation of commercially available small RNASeq library preparation kits using low input RNA

BMC Genomics
PMCID: 5936030
PMID: 29728066
DOI: 10.1186/s12864-018-4726-6

[…] The raw sequence image files from the Illumina HiSeq 2500 or Illumina MiSeq in the form of .bcl are converted to the fastq format using bcltofastq v1.8.4 and checked for quality to ensure the quality scores do not deteriorate drastically at the read ends. The adapters from the 3′ end are clipped using cutadapt v.1.10 [] (http://cutada […]


Robust Sub nanomolar Library Preparation for High Throughput Next Generation Sequencing

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

[…] Fastq files obtained from MiSeq and HiSeq 2500 sequencers were generated using MiSeq Reporter v. and CASAVA v.1.8.2 (or later, bcl2fastq v.2.2.0), respectively. Only those reads passing the chastity filter were reported. Data analyses performed at our core facility are briefly summarized below, and data analyses of mRNA- and […]


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