bcl2fastq2
- Version:
2.20.0
- Category:
bio
- Cluster:
Loki
Description
A utility that performs BCL conversion and demultiplexing in a single step
Documentation
Usage:
bcl2fastq2 [options]
Command-line options:
-h [ --help ] produce help message and exit
-v [ --version ] print program version information
-l [ --min-log-level ] arg (=INFO) minimum log level
recognized values: NONE, FATAL, ERROR, WARNING, INFO, DEBUG, TRACE
-i [ --input-dir ] arg (=<runfolder-dir>/Data/Intensities/BaseCalls/)
path to input directory
-R [ --runfolder-dir ] arg (=./) path to runfolder directory
--intensities-dir arg (=<input-dir>/../) path to intensities directory
If intensities directory is specified, --input-dir must also be specified.
-o [ --output-dir ] arg (=<input-dir>) path to demultiplexed output
--interop-dir arg (=<runfolder-dir>/InterOp/) path to demultiplexing statistics directory
--stats-dir arg (=<output-dir>/Stats/) path to human-readable demultiplexing statistics directory
--reports-dir arg (=<output-dir>/Reports/) path to reporting directory
--sample-sheet arg (=<runfolder-dir>/SampleSheet.csv)
path to the sample sheet
-r [ --loading-threads ] arg (=4) number of threads used for loading BCL data
-p [ --processing-threads ] arg number of threads used for processing demultiplexed data
-w [ --writing-threads ] arg (=4) number of threads used for writing FASTQ data.
This should not be set higher than the number of samples. If set =0 then these threads will be placed in the same pool as the loading
threads, and the number of shared threads will be determined by --loading-threads.
--tiles arg comma-separated list of regular expressions to select only a subset of the tiles available in the flow-cell. Multiple entries allowed, each
applies to the corresponding base-calls.
For example:
* to select all the tiles ending with '5' in all lanes:
--tiles [0-9][0-9][0-9]5
* to select tile 2 in lane 1 and all the tiles in the other lanes:
--tiles s_1_0002,s_[2-8]
--minimum-trimmed-read-length arg (=35) minimum read length after adapter trimming
--use-bases-mask arg specifies how to use each cycle.
--mask-short-adapter-reads arg (=22) smallest number of remaining bases (after masking bases below the minimum trimmed read length) below which whole read is masked
--adapter-stringency arg (=0.9) adapter stringency
--ignore-missing-bcls assume 'N'/'#' for missing calls
--ignore-missing-filter assume 'true' for missing filters
--ignore-missing-positions assume [0,i] for missing positions, where i is incremented starting from 0
--ignore-missing-controls (deprecated) assume 0 for missing controls
--write-fastq-reverse-complement generate FASTQs containing reverse complements of actual data
--with-failed-reads include non-PF clusters
--create-fastq-for-index-reads create FASTQ files also for index reads
--find-adapters-with-sliding-window find adapters with simple sliding window algorithm
--no-bgzf-compression turn off BGZF compression for FASTQ files
--fastq-compression-level arg (=4) zlib compression level (1-9) used for FASTQ files
--barcode-mismatches arg (=1) number of allowed mismatches per index
Multiple, comma delimited, entries allowed. Each entry is applied to the corresponding index; last entry applies to all remaining indices.
Accepted values: 0, 1, 2.
--no-lane-splitting do not split fastq files by lane.
Examples/Usage
Load the Anaconda module:
$ module load bio/bcl2fastq2/2.20.0-GCC-11.2.0
Check the loaded modules:
$ module list
List available modules:
$ module avail bcl2fastq2
Unload the Anaconda module:
$ module unload bio/bcl2fastq2/2.20.0-GCC-11.2.0
Installation
Source code is obtained from Bcl2fastq2