example.specs

Paired_end_reads:	1	{enter 1 for single-end reads, 2 for paired-ends}
Directory_path:	RAD18A/	{for parallel run only, enter location of files for run relative to user's home directory; leave blank for single processor run}
Read_length:	100	{enter read length for each read}
Input_file1:	RAD018A	{enter base file name for read 1: e.g., for RAD005R1.qseq, enter RAD005R1}
Input_file2:		{enter base file name for read 2 or leave blank for single read}
Samples_file:	RAD18a.index	{enter name of tab-delimited file with barcode_name, barcode_sequence, and individual SampleIDs}
Barcode_correction:	False	{enter True to turn on barcode correction}
Recode_quality_scores:	False	{enter True if your data are Illumina version 1.3/1.5 (Phred+64), "True" converts scores to version 1.8 (Phred+33)}
Restriction_site#1:	TGCAGG	{include only portion expected in RAD tag sequence}
Restriction_site#1:	CCTGCAGG	{full sequence of restriction site}
Restriction_site#2:	GAATT	{include only portion expected in RAD tag sequence}
Restriction_site#2:	GAATTC	{full sequence of restriction site}
P1_adapter:	AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
P2_adapter:	AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG	{enter expected sequence on forward (top) strand at end of P1 read}
Parallel_run:	16	{enter 0 for single processor, enter number of processors for parallel run}
Host_list:		{for parallel run only, list host machines on following lines - list multicore machines as many times as there are available cores; assumes connection via ssh}
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