Difference between revisions of "Bcl2Fastq/BCLconvert"
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:NGS]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
| − | |{{#vardefine:app|bcl2fastq}} | + | |{{#vardefine:app|bcl2fastq/bclconvert}} |
| − | |{{#vardefine:url|http://support.illumina.com/downloads/bcl2fastq_conversion_software.html}} | + | |{{#vardefine:url|http://support.illumina.com/downloads/bcl2fastq_conversion_software.html}}' |
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
| − | bcl2fastq conversion software can be used to both demultiplex data and | + | bcl2fastq: bcl2fastq conversion software can be used to both demultiplex data and |
convert BCL files to FASTQ files. This software requires a Linux operating | convert BCL files to FASTQ files. This software requires a Linux operating | ||
system. The bcl2fastq2 software can be used to convert BCL files from all | system. The bcl2fastq2 software can be used to convert BCL files from all | ||
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longer correct. For conversion of data generated on Illumina sequencing | longer correct. For conversion of data generated on Illumina sequencing | ||
systems using versions of RTA before RTA 2.0, use bcl2fastq v1.8.4. | systems using versions of RTA before RTA 2.0, use bcl2fastq v1.8.4. | ||
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| + | BCL convert: The Illumina BCL Convert v4.0 is a standalone local software app that converts the | ||
| + | Binary Base Call (BCL) files produced by Illumina sequencing systems to FASTQ files. BCL Convert v4.0 also | ||
| + | provides adapter handling (through masking and trimming), unique molecular identifier (UMI) trimming, and | ||
| + | produces metric outputs. | ||
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| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
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Latest revision as of 13:49, 8 January 2025
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Description
bcl2fastq: bcl2fastq conversion software can be used to both demultiplex data and convert BCL files to FASTQ files. This software requires a Linux operating system. The bcl2fastq2 software can be used to convert BCL files from all Illumina sequencing systems running RTA version 2.0 and above. This is a change from the original information, which indicated that v2.16 could be used with all sequencers running RTA 1.18 and above: that information is no longer correct. For conversion of data generated on Illumina sequencing systems using versions of RTA before RTA 2.0, use bcl2fastq v1.8.4.
BCL convert: The Illumina BCL Convert v4.0 is a standalone local software app that converts the Binary Base Call (BCL) files produced by Illumina sequencing systems to FASTQ files. BCL Convert v4.0 also provides adapter handling (through masking and trimming), unique molecular identifier (UMI) trimming, and produces metric outputs.
Environment Modules
Run module spider bcl2fastq/bclconvert to find out what environment modules are available for this application.
System Variables
- HPC_BCL2FASTQ/BCLCONVERT_DIR - installation directory