suffixC is a simple C program to align a fastq against a shortish reference sequence (around 10kb) using a suffix tree allowing for a small number of mismatches. Partial alignments are preserved in a separate file, useful for finding chimeric reads. It is most useful as a prefilter to pull out reads for alignment using a slower, more accurate program.
To install, download the repository (or git clone) and run make in the resulting directory:
wget https://github.com/sherrillmix/suffixr/archive/master.zip
unzip master.zip
cd suffixc-master
make
Usage: ./suffixc ref.fa reads.fastq [-o suffixcOut] [-l 20] [-m 0] [-h]
first argument: a reference sequence in a fasta file (if this is much more than 10kb then we could get memory problems)
second argument: a fastq file containing the reads to search
-o: (optional) the output prefix for outfiles (default: suffixcOut)
-l: (optional) specify how long a match has to be considered a partial match. A partial match on both ends counts as a match (default: 20)
-m: (optional) specify how many mismatches to tolerate (default: 0)
-h: (optional) display this message and exit
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