fastq_demux is a simple program to demultiplex a FASTQ file or a pair of FASTQ files based on the barcodes present in the FASTQ headers.

• fastq_demux GitHub page

• Module Name: fastq_demux (see the modules page for more information)
• Unusual environment variables set
  • FD_HOME  installation directory
  • FD_BIN       executable directory
  • FD_SRC       source code directory
  • FD_DATA  sample data directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
[user@cn0911 ~]$module load fastq_demux 
[+] Loading singularity  3.10.5  on cn4208
[+] Loading fastq_demux  20230713
[user@cn0911 ~]$cp $FD_DATA*/*
[user@cn0911 ~]$fastq_demux --R1 dual-index_Undetermined_S0_L001_I1_001.fastq.gz --R2 dual-index_Undetermined_S0_L001_I2_001.fastq.gz --samplesheet ./samplesheet_dual_index.tsv
known_barcode   count   percent
GGGGGGGG+AGATCTCG       22      44.0
GAAGATTT+TTTACTCT       5       10.0
GAAGATTT+AAAACGCC       3       6.0
unknown_barcode count   percent
GGGGGGGG+AGAACTCG       2       4.0
GGGGGGGG+AGAACGCG       2       4.0
GAAGATTT+CCACTCCG       1       2.0
GGAGATTT+GGGGGGGG       1       2.0
TAAGATTT+TAATCTCT       1       2.0
TAATATTT+TAAACGCT       1       2.0
TTATATTT+TAAACGCT       1       2.0
TCAGGGGG+AGATCTCG       1       2.0
TAATATTT+CCCACGCC       1       2.0
GAAGATTT+AAAACGCG       1       2.0

[user@cn0911 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$