/usr/share/doc/ray/Documentation/Illumina.txt is in ray-doc 2.3.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | # How to use Ray with Illumina reads
Illumina reads are readily usable.
Example with reads from all instruments:
mpiexec -np 9999 Ray \
-p Solexa_oldschool_reads_1.fastq Solexa_oldschool_reads_2.fastq \
-p Illumina_Genome_Analyzer_reads_1.fastq Illumina_Genome_Analyzer_reads_2.fastq \
-p Illumina_Genome_Analyzer_II_reads_1.fastq Illumina_Genome_Analyzer_II_reads_2.fastq \
-p Illumina_Genome_Analyzer_IIx_reads_1.fastq Illumina_Genome_Analyzer_IIx_reads_2.fastq \
-p Illumina_HiSeq_1000_TruSeq3_reads_1.fastq Illumina_HiSeq_1000_TruSeq3_reads_2.fastq \
-p Illumina_HiSeq_2000_TruSeq3_reads_1.fastq Illumina_HiSeq_2000_TruSeq3_reads_2.fastq \
-p Illumina_MiSeq_TruSeq3_reads_1.fastq -p Illumina_MiSeq_TruSeq3_reads_2.fastq
|