BCL2FASTQ Conversion Software pipeline

BCL2FASTQ Conversion Software specifications


Unique identifier OMICS_07545
Name BCL2FASTQ Conversion Software
Alternative names bcl2fastq2, bcl2fastq, CASAVA
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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BCL2FASTQ Conversion Software IN pipelines

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 213 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 (5) was used for as […]

PMCID: 5783200
PMID: 29298427
DOI: 10.1016/j.celrep.2017.12.039

[…] hiseq 2500 with single-end 50-bp reads at 25–60 million reads per sample., raw sequencing data were demultiplexed and converted into fastq files using consensus assessment of sequence and variation (casava) (v1.8.2) and quality-tested with fastqc v0.11.2. analysis was done in r v3.1.1 with bio-conductor package v2.13. alignment to the mm10 genome was performed using the spliced transcripts […]

PMCID: 5784596
PMID: 29368589
DOI: 10.1186/s12881-018-0525-9

[…] (pe100) in one lane of the hiseq2000 platform. sequence data analysis was performed using a bioinformatics pipeline developed in a previous study [3]. briefly, the illumina analysis pipepline (casava1.8) was employed for base calling. we then separated each barcoded dataset and removed the low-quality data using in-house scripts. the sequencing reads were subsequently aligned […]

PMCID: 5786528
PMID: 29403497
DOI: 10.3389/fimmu.2018.00015

[…] on the solexa platform. the sequence was directly determined using sequencing-by-synthesis technology via a truseq sbs kit. raw sequences were obtained from the illumina pipeline software, bcl2fastq v2.0, which was expected to generate 20 × 106 reads per sample., initially, the sequences generated were subjected to a filtering process to obtain qualified reads. trimmomatics […]

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