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+# kmer_id
+Mitichondrial read identification by kmer database for Galaxy server
+
+File kmer_read_m3.cpp
+uses gzip library, compile with:
+g++ -O3 -std=c++0x kmer_read_m3.cpp -o kmerread -lz
+
+database files needed in same directory:
+(can create with kmer_build, but not described here yet)
+mitochondria_data.txt
+mitochondria_refkey.txt
+mitochondria_count.txt
+mitochondria_tree.txt
+mitochondria_probes.txt.gz
+1a.fasta (test input)
+
+File kmer_read_m3.py  
+(Python 2.7)
+Run with:
+python kmer_read_m3.py -w [working directory] -d [output directory] -i [input filename1] [input filename2]
+
+Input files can be two paired files (.fastq, .fastq.gz, .fasta, .fasta.gz) or a single file with none as filename2
+Output is .csv file with read count and % abundance for each species.