WannaAln takes in a pair of FASTQ file and an arbitary length pattern, calculates the edit distance of 4 pairs including "R1 x pattern", "R2 x pattern", "R1 x ReverseComplement(pattern)" and "R2 x ReverseComplement(pattern)", and output the reads to a pair of new FASTQ file if any of the 4 edit distances go below a threshold.
wannaAln
Ruibang Luo
rluo5@jhu.edu
-a [STR] Input R1
-b [STR] Input R2
-x [STR] Output R1, gzipped
-y [STR] Output R2, gzipped
-p [STR] Matching pattern
-m [INT] Edit distance allowed, default 1
-h Show help information
https://github.com/aquaskyline/WannaAln.git
cd WannaAln
make
cd test
sh test.sh