Calls to run QC pipeline and Trinity assembler

- build contaminants index
% bowtie2-build -f montastraea_franksi_rrna_mtrna_contaminants.fasta,savalia_savaglia_rrna_mtrna_contaminants.fasta,actiniaria_rrna_mtrna_contaminants.fasta,nematostella_rrna_mtrna_contaminants.fasta,clathrina_rrna_mtrna_contaminants.fasta /path/to/contam_dir/contaminants_index

- construct alignments
% export BOWTIE2_INDEXES=/path/to/contam_dir/
% bowtie2 -q --phred33 --quiet --very-sensitive -t -p 2 -x contaminants_index -U input.fastq --un temp.fastq > /dev/null

- remove technical artifacts
% fastx_artifacts_filter -Q33 -i temp.fastq -o temp2.fastq

- trim GC content from beginning
% fastx_trimmer -Q33 -f <first_index_to_keep> -i temp2.fastq -o temp.fastq

- adaptive trimming using quality values
% btrim64-static -q -a 30 -t temp.fastq -o output.fastq -s summary_file.btrim -S

- Split files into paired reads to be inputed into Trinity.
- The previous steps may have removed one of the paired reads from a fragment.
- Ensure that the input to trinity correctly represents the paired reads and newly created unpaired reads.

- run trinity assembler
% Trinity.pl --run_butterfly --CPU 8 --seqType fq --left output_left.fastq --right output_right.fastq --SS_lib_type RF --paired_fragment_length 328