BCL2FASTQ Conversion Software specifications


Unique identifier OMICS_07545
Name BCL2FASTQ Conversion Software
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 citations

PMCID: 5917026

[…] 2500 sequencer using the truseq v4 cluster and sbs sequencing kits, respectively (paired-end; 2 × 125 cycles). demultiplexing and generation of fastq files was performed using scripts from illumina (bcl2fastq v.1.8). fastqc (v0.11.5)56 was used to assess read quality, gc content, the presence of adaptors, over-represented k-mers and duplicated reads. bases with low quality score were removed […]

PMCID: 5904157

[…] each lane, which yields targeted number of single-end 100 bp reads for each sample, as a fraction of 180 million reads for the whole lane. rta software (illumina, usa) was used for base calling and bcl2fastq (version 1.8.4) for converting bcl to fastq format, coupled with adaptor trimming. the reads were mapped to a reference genome (mouse: ucsc/mm9) using tophat20 (version 2.0.4) with four […]

PMCID: 5896988

[…] as single-end, 50-nucleotide reads. library preparation, quality control, and sequencing were performed by the nyulmc genome technology center., sequence files were generated in fastq format by bcl2fastq version 1.8.4 [30]. greater than 95% of all base pairs in all samples had a q score of 30, which corresponds to a calling accuracy of 99.9%. 76.6 million to 95.9 million qualified, 50bp […]

PMCID: 5851642

[…] of the library. the sequence was directly determined by the sequencing-by-synthesis technology using the truseq sbs kit (illumina). raw sequences were obtained from the illumina pipeline software bcl2fastq v2.0, which was expected to generate 10 million reads per sample., the generated sequences were filtered to obtain good quality reads. trimmomatics was implemented to trim or remove […]

PMCID: 5861150

[…] torrent gives output in three formats—bam, fastq, or vcf. each of these has to be converted to fasta or fastq format either by running scripts that are part of the software platform (sffinfo-roche; bcl2fastq-illumina) or by using one of the many freely available scripts (bamtofastq, sff_extract). fasta and fastq are the two common input formats for most analysis programs. fasta format consists […]

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