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annotate README.md @ 2:a0852bb4b09b draft

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author cstrittmatter
date Thu, 25 Apr 2019 07:59:05 -0400
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1 # kmer_id
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2 Mitichondrial read identification by kmer database for Galaxy server
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4 File kmer_read_m3.cpp
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5 uses gzip library, compile with:
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6 g++ -O3 -std=c++0x kmer_read_m3.cpp -o kmerread -lz
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7
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8 database files needed in same directory:
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9 (can create with kmer_build, but not described here yet)
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10 mitochondria_data.txt
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11 mitochondria_refkey.txt
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12 mitochondria_count.txt
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13 mitochondria_tree.txt
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14 mitochondria_probes.txt.gz
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15 1a.fasta (test input)
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16
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17 File kmer_read_m3.py
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18 (Python 2.7)
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19 Run with:
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20 python kmer_read_m3.py -w [working directory] -d [output directory] -i [input filename1] [input filename2]
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21
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22 Input files can be two paired files (.fastq, .fastq.gz, .fasta, .fasta.gz) or a single file with none as filename2
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23 Output is .csv file with read count and % abundance for each species.