Cross-align a sequencing run against possible library to check for contamination.
crossAlign.sh <FASTQDIR> <FASTA>, where <FASTQDIR> is a directory containing fastq.gz files, and
<FASTA> is a FASTA file containing all expected reference sequences.
A FASTA file with the PhiX genome can be found in phix.fasta.
Another tool, parajson2fasta.R is provided to automatically extract
tile sequences from tileseq parameter sheets into a FASTA file.
parajson2fasta.R [-o <OUTFILE>] <JSONDIR>