# Remove adaptor from sequences and produce a number of plots.
-# Usage: read_fastq -i test.fq | remove_adaptor.sh | write_fastq -xo test_no_adaptor.fq
+# Usage: read_fastq -i test.fq | remove_adaptor_454.sh | write_fastq -xo test_no_adaptor.fq
adaptor='TCGTATGCCGTCTTCTGCTTG' # 454 adaptor
pid=$$
-#find_adaptor -a $adaptor |
plot_lendist -t post -o 00_remove_adaptor_lendist_seq_before.$pid.ps -k SEQ_LEN |
-parallel -k --blocksize 50M --pipe --recend "\n---\n" "nice -n 19 find_adaptor -a $adaptor" |
+find_adaptor -a $adaptor -p |
plot_histogram -t post -o 01_remove_adaptor_histogram_adaptor_pos.$pid.ps -k ADAPTOR_POS -s num |
plot_lendist -t post -o 02_remove_adaptor_lendist_adaptor_len.$pid.ps -k ADAPTOR_LEN |
plot_lendist -t post -o 03_remove_adaptor_lendist_seq_after.$pid.ps -k SEQ_LEN |