Hi I have generated some random DNA reads and want to send them to Bow Tie as a .txt file and retrieve output with the DNA codes that cannot be aligned for a given reference genome. I would appreciate if anyone working on it could send me an api in java to send short reads to Bow tie remotely to see the non aligned reads. Thank you in advance.
Bowtie reads fastq files. http://en.wikipedia.org/wiki/FASTQ_format
Bowtie produces BAM files: You can filter a BAM file with samtools to extract the unmapped reads.
You can call Bowtie from java http://www.mkyong.com/java/how-to-execute-shell-command-from-java/
remotely ?: you can always code a java server calling bowtie (good luck !) : http://plindenbaum.blogspot.fr/2013/04/java-jni-bindings-for-bwamem-lite.html