diff --git a/docs/tutorial.md b/docs/tutorial.md index fee32ac..7f68326 100644 --- a/docs/tutorial.md +++ b/docs/tutorial.md @@ -25,7 +25,7 @@ The aims are: Use conda to set up an environment with all the software we need for this tutorial: ``` -conda create -n grootTutorial -c bioconda parallel==20171222 sra-tools==2.8 fastqc==0.11.7 bbmap==37.90 multiqc==1.4 groot==0.3 seqkit==0.7.2 samtools==1.4 metacherchant==0.1.0 +conda create -n grootTutorial -c bioconda parallel==20171222 sra-tools==2.8 fastqc==0.11.7 bbmap==37.90 multiqc==1.4 groot==0.7 seqkit==0.7.2 samtools==1.4 metacherchant==0.1.0 source activate grootTutorial ``` @@ -123,7 +123,7 @@ Download the pre-clustered [ARG-ANNOT](http://en.mediterranee-infection.com/arti groot get -d arg-annot ``` -Index the ARG-ANNOT database: +Index the database: ``` bash groot index -i arg-annot.90 -o groot-index -l 100 -p 8 @@ -136,11 +136,12 @@ groot index -i arg-annot.90 -o groot-index -l 100 -p 8 Align the reads against the index: ``` bash -ls *.fastq | parallel --gnu "groot align -i groot-index -f {} -p 8 > {/.}.bam" +ls *.fastq | parallel --gnu "groot align -i groot-index -f {} -p 8 -o {/.}-groot-graphs > {/.}.bam" ``` * for each sample, the align subcommand produces a BAM file containing all graph traversals for each read * each BAM file essentially contains the ARG-derived reads in each sample +* the graphs (`.gfa`) which had reads align are stored in a separate directory for each sample (`-o {/.}-groot-graphs`) ### 4.a. Compare ARG diversity diff --git a/paper/benchmarking/accuracy/run_accuracy_test.sh b/paper/benchmarking/accuracy/run_accuracy_test.sh index 667f99b..0aaeae8 100644 --- a/paper/benchmarking/accuracy/run_accuracy_test.sh +++ b/paper/benchmarking/accuracy/run_accuracy_test.sh @@ -16,7 +16,7 @@ # # test parameters -THREADS=8 +THREADS=1 READ_LEN=150 K_SIZE=7 SIG_SIZE=128 diff --git a/paper/benchmarking/mock-metagenome/run_benchmark.sh b/paper/benchmarking/mock-metagenome/run_benchmark.sh index 7081737..88ed798 100644 --- a/paper/benchmarking/mock-metagenome/run_benchmark.sh +++ b/paper/benchmarking/mock-metagenome/run_benchmark.sh @@ -15,7 +15,11 @@ # bioawk (conda install bioawk) # BBMap # Go 1.9 +# Perl # gtime (brew install gnu-time) +# git +# Nextflow (for amr-plusplus) +# Docker (for amr-plusplus) # test parameters COVERAGE=$1 @@ -54,13 +58,11 @@ echo "creating artificial metagenome..." tail -n +1 *.fna > genomes.fna sed '/^==>/ d' < genomes.fna > ../groot-reference-data.fna cd .. -randomreads.sh ref=groot-reference-data.fna len=${READ_LEN} out=groot-reads.fq metagenome=true coverage=${COVERAGE} adderrors=true maxsnps=0 maxinss=0 maxdels=0 maxsubs=0 > /dev/null 2>&1 -wget http://kirill-kryukov.com/study/tools/fastq-splitter/fastq-splitter-0.1.2.zip -unzip fastq-splitter-0.1.2.zip -perl fastq-splitter.pl --n 2 groot-reads.fq -mv groot-reads.fq.part-1 groot-reads_1.fq -mv groot-reads.fq.part-2 groot-reads_2.fq -rm groot-reads.fq fastq-split* +randomreads.sh ref=groot-reference-data.fna len=$((${READ_LEN} * 2)) out=groot-reads.fq metagenome=true coverage=${COVERAGE} adderrors=true maxsnps=0 maxinss=0 maxdels=0 maxsubs=0 > /dev/null 2>&1 +perl ../splitFASTQ.pl groot-reads.fq +mv groot-reads.fq_1 groot-reads_1.fq +mv groot-reads.fq_2 groot-reads_2.fq +rm groot-reads.fq # install GROOT echo "installing GROOT..." @@ -107,6 +109,12 @@ mv argsOAP-output/extracted.fa ../argOAP-upload/ && mv argsOAP-output/meta_data_ cd .. echo "argsOAP stage 1 finished - upload the 2 files in the 'argOAP-upload' directory to http://smile.hku.hk/SARGs and run argsOAP stage 2" +# run AMRplusplus +echo "running AMRplusplus..." +git clone https://github.com/cdeanj/amrplusplus ./amrplusplus && cd amrplusplus +nextflow run main.nf --reads "../groot*{1,2}.fq" --amr ../../../../../db/full-ARG-databases/card/card-1.1.2.fna --output ../amrplusplus-results -profile docker --threads $THREADS --threshold 100 +echo "AMRplusplus finished - results are in 'amrplusplus-results'" + # clean up grep ">" source_genomes/randomARGs.fna > ./spiked-ARGS.fna yes | rm -r groo* source_genome* ref Ublastx_stageone* diff --git a/paper/benchmarking/mock-metagenome/splitFASTQ.pl b/paper/benchmarking/mock-metagenome/splitFASTQ.pl new file mode 100644 index 0000000..cb765a0 --- /dev/null +++ b/paper/benchmarking/mock-metagenome/splitFASTQ.pl @@ -0,0 +1,21 @@ +use strict; +use warnings; +my $file = $ARGV[0]; +open(FILE, "<$file") || die "cannot open $file\n"; +open(OUT1, ">$file\_1") || die "cannot open $file\_1\n"; +open(OUT2, ">$file\_2") || die "cannot open $file\_2\n"; +while(){ + chomp; + print OUT1 "$_\/1\n"; + print OUT2 "$_\/2\n"; + my $newline = ; chomp($newline); + print OUT1 substr($newline, 0, length($newline)/2)."\n"; + print OUT2 substr($newline, length($newline)/2, length($newline)/2)."\n"; + $newline = ; chomp($newline); + print OUT1 "$newline\/1\n"; + print OUT2 "$newline\/2\n"; + $newline = ; chomp($newline); + print OUT1 substr($newline, 0, length($newline)/2)."\n"; + print OUT2 substr($newline, length($newline)/2, length($newline)/2)."\n"; +} +close(FILE); diff --git a/paper/benchmarking/spiked-ARGs.fna b/paper/benchmarking/spiked-ARGs.fna new file mode 100644 index 0000000..aab0763 --- /dev/null +++ b/paper/benchmarking/spiked-ARGs.fna @@ -0,0 +1,20 @@ +>vanRD.3002923.AY082011.0-699.122 +ATGAATGAAAAAATCTTAGTGGTTGACGATGAAAAAGAGTTGGCCGACTTAGTTGAAGTGTACCTGAAAAACGATGGATATACCGTTTATAAATTTTATAATGGCAGGGACGCATTAAATTGCATTGAATCCGTGGAACTGGATTTAGCCATACTGGATATCATGCTCCCGGATATTGACGGTTTTCAAATCTGCCAGAAAATCCGGGAGAAGTTCTACTTCCCTGTTATCATGCTGACAGCGAAAGTAGAAGATGGGGATAAAATCATGGGGCTGTCCGTTGCAGATGATTATATTACGAAGCCGTTTAATCCGCTGGAAGTGGTTGCGAGGGTAAAGGCACAGCTAAGGCAGTACATGCGGTACAAGCAGCCCTGCATAAAGCAGGAGGCTGAACGCACGGAATACGATATCCGGGGGATGACAATCAGCAAGAGCAGCCATAAGTGTATCTTGTTTGGAAAGGAAATTCAACTGACACCAACGGAATTTTCGATCCTTTGGTATCTGTGCGAGCGTCAGGGAACGGTAGTTTCTACGGAGGAATTATTCGAGGCAGTATGGGGCGAGCGGTATTTTGACAGCAATAATACCGTGATGGCGCATATTGGGCGTCTCAGAGAGAAAATGAAGGAACCGTCAAGAAACCCGAAGTTCATAAAAACCGTGTGGGGAGTTGGATATACCATTGAAAAATAAA +>OXA-131.3001652.EU547446.0-825.1678 +ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTGTTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCAACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG +>parC.3003925.NC_015964.1.1905162-1907418.3728 +ATGAGCAATATTAATTACGAAGGCATCGAGCAGATGCCACTTCGCACCTTTACAGAAAAGGCTTACCTTAATTATTCAATGTACGTCATCATGGATCGTGCATTGCCTTTTATTGGCGATGGCTTAAAGCCTGTTCAACGTCGTATTGTCTATGCGATGTCTGAACTGGGTTTAAATGCCGCGGCAAAATTTAAAAAGTCCGCGCGTACCGTCGGTGATGTGTTAGGTAAATTCCATCCACATGGTGACTCTGCTTGTTATGAAGCCATGGTATTAATGGCTCAGCCTTTTTCTTATCGTTATCCTTTGGTAGATGGGCAAGGAAACTGGGGGGCGCCAGATGATCCTAAATCATTTGCGGCAATGCGTTATACAGAATCTCGCCTGTCCAAAATCTCTGAAATTTTATTATCTGAATTAGGCCAAGGCACTGTTGATTTCCAACCGAACTTTGATGGTACCTTAGAAGAACCTCAATATTTGCCTGCACGTTTGCCTCATATTCTGTTAAACGGCACCACCGGGATTGCCGTCGGGATGGCAACCGATATTCCACCACATAATATTAATGAAGTGGCGGATGCCGCTGTTATGCTATTAGATAATCCAAAAGCAGGATTAGATGATGTACTCAATATCATTCAAGGCCCGGATTTCCCAACTGAAGCGGAAATTATTTCACCAAAAGATGATATTCGCAAAATGTATGAAACCGGTCGTGGTTCTATCAAAATGCGTGCAACATGGCATAAAGAAGACGGTGAAATCATCATTAGTGCACTTCCTCATCAATCTTCACCATCAAAAATCATTGCGCAAATTGCTGAACAAATGACAGCAAAAAAATTGCCAATGGTGGAAGATATTCGTGATGAAGCAGATTATGAAAACCCTGTACGTATCGTGCTTGTGCCACGTTCAAATCGTGTTGATACGGATGCCTTAATGGCGCATTTATTTGCGACGACTGATCTCGAAAAAAGCTATCGTGTAAATATGAATATGATCGGACTTGATCATAAACCAGCCGTAAAAGGCCTACTTCAAGTTCTTATCGAATGGCTGACATTCCGTCGTACTACCGTGACACGTCGTTTACAACATCGTTTAGATAAAGTACTCGCTCGTTTGCACATTTTAGATGGTTTGATGATTGCCTTCCTCAATATTGACGAAGTGATTGAGATTATTCGTACTGAAGATGAACCAAAACAAGTTTTAATGGCTCGCTTTAACTTAAGTGATGAACAGGCAGAAGCCATTTTAAACTTACGTTTACGCCATTTGGCCAAATTAGAAGAACATCAATTACAAGCTGAAAAAGATAAACTCGAAGAAGAGCGGTCAAATTTAGAGTTAATTTTAGGATCTGAACGTCGCTTAAATACCTTGATCAAAAAAGAAATTCAAGAAGATGCGAAAAAATACGCCAGCCCTAGAATGTCTCAATTAGTTGAACGTGAAGAAGCGAAAGCCATTTCTGAAAGTGAAATGACTCCGGCTGAACCCGTTACCGTTATCTTATCTGAAATGGGCTGGGTACGCTGTGCAAAAGGTCATGACATTGATCCGGAAGGATTAAGCTATAAAGCAGGCGATAAATATCTGGCTCACGCTTGCGGTAAAAGTAATCAGCCTGTAATCTTTATTGACAGCACGGGGCGTAGCTATGCTTTAGATCCATTAAGCTTGCCTTCTGCGCGTTCACAAGGTGAACCACTCACCGGTAAACTGACATTACCGGCCGGTGCGACCATTGAACAGGTTATTATGGAACCTGAAAAACAAGAATTATTGATGGCATCAGATGCAGGATATGGTTTTATTTGCAAATTTGAAGATTTAATTGCGCGTAATAAAGCAGGAAAAGCCTTGATTTCTTTGCCAGAAAATGCGAAAGTCTTGAAACCTGAGACACTTTCCGAGTCGACCTCACTTCTTGTGTCCCTCACTTCAGCGGGTCGAATGCTGATTTTTCCGGTACGGGATTTACCGGCATTATCAAAAGGGAAAGGCAACAAAATCATCAGTATTCCAGCAGCGAATGCAAAAGCGCGGTCAGAATTATTAGTGAAATTGTTCTTAATTTCAGAGCAAGCTAGCCTTGAGTTCCATTCCGGTAAACGAAAAATCACATTAAAACCGGAAGATCTGCAAAAATTCCGAGCGGAACGCGGCAGAAAAGGCTCCCAATTACCACGTGGATTACATAGCAATGTTGATATTGTGGTAGTTGAACCCGAACACAACTCATAA +>CTX-M-5.3001868.U95364.5-881.1087 +ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCACGCGCAGACGAACAGCGTGCAGCAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGGCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGGAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGCAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATGTTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGAT +>OXA-118.3001768.AF371964.118-919.965 +ATGGCAATCCGATTCCTCACCATACTGCTATCTACTTTTTTTCTTACCTCATTCGTGCATGCGCAAGAACACGTGCTAGAGCGTTCTGACTGGAAGAAGTTCTTCAGCGACCTCCGGGCCGAAGGTGCAATCGTTATTTCAGACGAACGTCAAGCGGAGCATGCTTTATTGGTTTTTGGTCAAGAGCGAGCAGCAAAGCGTTACTCGCCTGCTTCAACCTTCAAGCTTCCACACACACTTTTTGCACTCGATGCAGACGCCGTTCGTGATGAGTTCCAGGTTTTTCGATGGGACGGCGTTAAACGGAGCTTTGCGGGCCATAATCAAGACCAAGACTTGCGATCAGCGATGCGAAATTCTGCGGTCTGGGTTTATGAGCTATTTGCAAAAGAGATCGGAAAGGACAAAGCAAGACACTATTTAAAGCAAATTGATTATGGCAACGCCGACCCTTCGACAATCAAGGGCGATTACTGGATAGATGGCAATCTTGAAATCTCAGCGCACGAACAGATTTCGTTTCTCAGAAAACTCTATCGAAATCAGCTGCCATTTCAGGTGGAACATCAGCGCTTGGTCAAAGATCTCATGATTACGGAAGCCGGGCGCAACTGGATACTACGCGCAAAGACCGGCTGGGAAGGCAGGTTTGGCTGGTGGGTAGGGTGGGTGGAGTGGCCAACCGGTCCCGTATTCTTCGCGCTGAATATTGATACGCCAAACAGAACGGATGATCTTTTCAAAAGAGAGGCAATCGCGCGGGCAATCCTTCGCTCTATCGACGCATTGCCGCCCAACTAAT +>OXA-363.3001550.KF460533.0-831.890 +ATGAAAACTCTGATTTTTCTGCCTTTACTTAATTGCTTGAGCCTGACGGCGTGTACCTTACCCGTTTCATCTTCCCCATCTCATATCACTTCGACTCAATCGACTCAAGCCATTGCCCAATTATTTGATCAGGCGCAAAGCTCTGGCGTTTTAGTGATTCAGCGTGGTCAACAGATACAGGTCTATGGCAATGATTTAAGCCGTGCAGATACCGAATATGTTCCCGCCTCTACTTTTAAAATGCTCAATGCCCTGATTGGCCTGCAACATGGCAAAGCCACAACCAATGAAATTTTTAAATGGGATGGTAAGAAACGTAGTTTTTCAGCCTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCTTCTGCTGTACCCGTCTATCAGGAACTGGCGCGTCGTATTGGCCTTGAACTGATGCAACAGGAAGTACAACGCATCCAATTTGGTAATCAGCAGATTGGTCAGCAAGTCGATAATTTCTGGTTGGTAGGCCCTTTGAAAATCACTCCAAAACAGGAGGTCGAATTTGTCTCGGCTCTAGCCCGAGAGCAGCTTGCCTTTGATCCACAAGTCCAGCAGCAAGTCAAAGCCATGTTACTTTTACAGGAGCGGAAAGCTTATCGACTATATGCCAAATCTGGTTGGGGCATGGATGTGGAACCACAAGTCGGCTGGCTCACCGGCTGGGTTGAAACACCGCAGGCTGAAATCGTGGCATTTTCGCTGAATATGCAGATGCAAAATGGTATGGATCCGGCAATCCGCCTTGAAATTTTACAGCAGGCTTTGGCCGAATTAGGGCTTTATCCAAAAGCTGAAGGATGA +>OXA-108.3001639.EF650034.0-825.1367 +ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTACTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATACAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG +>OXA-192.3001766.JF273470.0-810.1756 +ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAACATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATACATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTTGAATCTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCACAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGGCTTGAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAATATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTGCCGTATCCTATAGAAATACAAAAAGCTGTTTCTGATATTACTATACTAGAGCAAACTGACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTGAAAACATGACAACTGAGCCTATTGGTTGGTTAGTAGGCTGGCTTGAAGAAAATAATAATATATACGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA +>OXA-214.3001713.JN861782.0-828.1208 +ATGAAGCTATCAAAATTATACACCCTCACTGTGCTCATAGGATTTGGATTAAGCGGTGTCGCCTGCCAGCATATCCATACTCCAGTCTCGTTCAATCAAATTGAAAACGATCAAACAAAGCAGATCGCTTCCTTGTTTGAGAATGTTCAAACAACAGGTGTTCTAATTACCTTTGATGGACAGGCGTATAAAGCATACGGTAATGATCTGAATCGTGCCAAAACTGCGTATATCCCAGCATCTACTTTCAAAATATTAAATGCTTTGATTGGCATTGAACATGATAAAACTTCACCAAATGAAGTATTTAAGTGGGATGGTCAGAAGCGTGCTTTTGAAAGTTGGGAAAAAGATCTGACTTTAGCTGAAGCCATGCAAGCTTCTGCTGTACCTGTTTATCAAGCGCTTGCCCAGAGAATCGGATTGGATTTGATGGCAAAGGAAGTCAAAAGAGTCGGCTTCGGTAATACACGCATCGGAACACAAGTTGATAACTTCTGGCTCATTGGACCTTTAAAGATCACGCCAATCGAAGAAGCTCAATTTGCTTACAGGCTTGCAAAACAGGAGTTACCGTTTACCCCAAAAACACAACAGCAAGTGATTGATATGCTGTTGGTGGATGAAATACGGGGAACGAAAGTTTACGCCAAAAGTGGTTGGGGAATGGATATTACCCCGCAAGTAGGATGGTGGACTGGATGGATTGAAGATCCGAACGGAAAAGTGATCGCTTTTTCTCTCAATATGGAAATGAATCAACCTGCGCATGCAGCTGCACGTAAAGAAATTGTTTATCAGGCACTTACGCAATTGAAATTATTGTAA +>ErmQ.3000593.L22689.261-1035.678 +ATGAAAGCTAAAAGTAATAATTATAGAGGAAAAGTTGATATTAGTGTATCGCAAAATTTTATTACTAGTAAAAATACTATATATAAATTAATAAAAAAAACAAATATATCCAAAAATGATTTTGTTATTGAAATTGGACCAGGAAAAGGTCATATAACAGAAGCTTTATGTGAAAAAAGTTATTGGGTTACAGCTATAGAACTAGATAGAAGTTTATATGGAAATTTAATAAATAAATTTAAAAGTAAAAATAATGTTACTCTTATTAATAAAGATTTTTTAAATTGGAAATTACCTAAAAAAAGAGAATATAAGGTATTTTCTAATATTCCTTTTTATATAACAACAAAGATTATTAAGAAATTATTATTAGAAGAGTTAAATTCACCAACTGATATGTGGCTAGTTATGGAGAAAGGTTCCGCAAAAAGATTTATGGGAATACCTAGAGAGAGTAAATTATCATTACTTTTAAAAACTAAATTTGATATTAAGATAGTGCACTATTTTAATAGAGAAGACTTCCATCCCATGCCTAGTGTAGATTGCGTCTTAGTATATTTTAAAAGAAAATATAAATATGATATATCTAAAGATGAATGGAATGAATATACAAGTTTTATATCTAAGTCTATTAATAACTTAAGAGATGTATTTACAAAAAATCAAATTCATGCAGTAATTAAATACCTAGGTATAAATCTTAATAATATTAGTGAAGTTTCTTATAATGATTGGATACAGTTATTTAGATATAAACAAAAGATAGATTAGT diff --git a/src/version/version.go b/src/version/version.go index 390352e..58f68a0 100644 --- a/src/version/version.go +++ b/src/version/version.go @@ -1,3 +1,3 @@ package version -const VERSION = "0.6" +const VERSION = "0.7"