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author cstrittmatter
date Fri, 12 Apr 2019 14:58:18 -0400
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1 # kmer_id
2 Mitichondrial read identification by kmer database for Galaxy server
3
4 File kmer_read_m3.cpp
5 uses gzip library, compile with:
6 g++ -O3 -std=c++0x kmer_read_m3.cpp -o kmerread -lz
7
8 database files needed in same directory:
9 (can create with kmer_build, but not described here yet)
10 mitochondria_data.txt
11 mitochondria_refkey.txt
12 mitochondria_count.txt
13 mitochondria_tree.txt
14 mitochondria_probes.txt.gz
15 1a.fasta (test input)
16
17 File kmer_read_m3.py
18 (Python 2.7)
19 Run with:
20 python kmer_read_m3.py -w [working directory] -d [output directory] -i [input filename1] [input filename2]
21
22 Input files can be two paired files (.fastq, .fastq.gz, .fasta, .fasta.gz) or a single file with none as filename2
23 Output is .csv file with read count and % abundance for each species.