This is a read demultiplexer. Pros: * Can manage a lot of mismatches == Motivation == The Illumina HiSeq 1000 dumps .cif (intensity) files, .bcl (base calls) files and .clocs (probably a summary of the intensities?)files, among others. Basically, for each cluster on the flow cell, there will be 4 sequences: R1, R2, R3, R4. R2 and R3 are the indexes, or bar-codes, and R1 and R4 are the sequences. There also may be only R1, R2, and R3 (RNA-Seq and ChIP-Seq) CASAVA 1.8.2 only allows 1 mismatch per index (2 for dual-indexes). Furthermore CASAVA 1.8.2 has been released many years ago. This demultiplexer allows more data to be retrieved and is maintained too ! This demultiplexer is implemented in Python as a single executable. This is GPL work. == Input files == The files can be in fastq or in fastq.gz. == Output files == fastq.gz == Conversion from BCL/CLOCS to FASTQ == #!/bin/bash #$ -N convert-HiSeq1000-BCL-2011-12-21.8 #$ -P nne-790-ab #$ -l h_rt=48:00:00 #$ -pe default 8 #$ -cwd sequenceWorld=/rap/nne-790-ab/Instruments/Illumina_HiSeq_1000_Hellbound run=111207_SNL131_0065_AC0947ACXX NSLOTS=8 source /rap/nne-790-ab/software/CASAVA_v1.8.2/module-load.sh configureBclToFastq.pl \ --input-dir $sequenceWorld/$run/Data/Intensities/BaseCalls \ --output-dir $sequenceWorld/$run/FastQ-Sequences/no-demul-Unaligned \ --use-bases-mask Y*,Y*,Y*,Y* cd $sequenceWorld/$run/FastQ-Sequences/no-demul-Unaligned make -j $NSLOTS == Demultiplexing FASTQ files == By now, you should have one directory per lane. [@colosse1 FastQ-Sequences]$ ls no-demul-Unaligned/Project_C0947ACXX/ -1 Sample_lane1 Sample_lane2 Sample_lane3 Sample_lane4 Sample_lane5 Sample_lane6 Sample_lane7 Sample_lane8 To demultiplex lane 7, run this: FastDemultiplexer.py SampleSheet.csv 7 Project_C0947ACXX/Sample_lane7 Demultiplexed > stat.txt This will generate Demultiplexed/Project_A/Sample_X Demultiplexed/Project_A/Sample_Y Demultiplexed/Project_A/Sample_Z ... and Demultiplexed/Undetermined_indices/Sample_lane7 == Author == SĂ©bastien Boisvert