Package: csstar
c-SSTARCLI-Sequence Search Tool for Antimicrobial ResistanceSystem RequirementsLinux or Mac OS X platformBLAST+ (blastn and makeblastdb)Python 2.7 or 3 with BioPythonUsagec-SSTAR -g <genome_file> -d <database_file>InputFastA formatted genomeFastA database of antimicrobial resistance (AR) gene sequences from SSTAR. Two databases are available (ARG-ANNOTorResFinder), which are formatted according to Kat Holt's clustering approach forSRST2. A combination of these two databases also exists"ResGANNOT"OutputI) Summary output (to stdout)A tab-delimited summary is printed to standard out with the following fields:AR gene family (from database)AR gene variant (from database)sequence defline/header where the AR gene is located (from genome)% nucleotide identity (from blastn output)bp length of alignment (from blastn output)bp length of AR gene (from blastn output)Columns 1 and 2 will have suffixes appended to denote special interest:*indicates the best scoring allele is full-length but has >=1 mismatch (SNP). This often means you have a novel allele.?indicates uncertainty in the result due to incomplete length alignmentTRindicates truncation due to an internal stop codon being present$indicates gene detected at edge of contigII) Raw alignment output (OUTDIR/BASENAME.blastn.tsv)The tab-delimited outfmt 6 of blast is saved with three columns added to the right. Column 13 is the query (AR gene database) length, column 14 is the subject (contig) length, and column 15 is the subject (contig's AR gene) sequence.III) Log output (OUTDIR/c-SSTAR_BASENAME.log)A text file is generated to log the date and time of execution, user ID, shell environment, python version, blastn binary location, and blastn version.Example Installpip install biopython
git clone https://github.com/chrisgulvik/c-SSTAR.git $HOME
echo 'export PATH="$PATH:$HOME/c-SSTAR"' >> $HOME/.bash_profileExample UsageRun c-SSTAR on several genomes with the combo databaseforFin*.fna;doB=$(basename$F.fna)c-SSTAR-g$F-d~/c-SSTAR/db/ResGANNOT_srst2.fasta.gz-o$B>"$B"_ResGANNOT.tabdoneExample Summary Outputc-SSTAR-g~/c-SSTAR/tests/data/SRR3112344.fa.gz\-d~/c-SSTAR/db/ResGANNOT_srst2.fasta.gzAR_FamilyAR_VariantQuery_DeflineIdentityAln_LenDB_Gene_Lenaac(3)*aac(3)-IId*tig09399.884%861861aac(3)?aac(3)-Ib-aac(6')-Ib'?tig12399.097%5541005aac(6')aac(6')-Ib-crtig123100.0%600600aac(6')?aac(6')-30-aac(6')-Ib'?tig12399.309%579987aadA2?aadA2?tig10499.875%802819ampH*ampH*tig00398.88%11611161aph(3'')*aph(3'')-Ib*tig09699.876%804804aph(6)*aph(6)-Id*tig09699.881%837837blaCTXblaCTX-M-15tig089100.0%876876blaOXAblaOXA-1tig123100.0%831831blaSHVblaSHV-11tig016100.0%861861blaSHV*blaSHV-100*tig01695.111%900900blaTEMblaTEM-1Btig108100.0%861861catA2*catA2*tig12796.106%642642catB3?$catB3?$tig123100.0%440633catB4?$catB4?$tig123100.0%440549dfrA12dfrA12tig104100.0%498498dfrA14*dfrA14*tig13499.586%483483fosA6?$fosA6?$tig02698.81%420433mph(A)?TRmph(A)?TRtig11099.675%922921oqxAoqxAtig024100.0%11761176oqxBoqxBtig024100.0%31533153qnrB1*TRqnrB1*TRtig08099.853%681681sul1*sul1*tig10499.885%867867sul2sul2tig096100.0%816816tet(D)tet(D)tig108100.0%11851185Literature Referencesc-SSTAR: Cunningham SA, Limbago B, Traczewski M, Anderson K, Hackel M, Hindler J, Sahm D, Alyanak E, Lawsin A, Gulvik CA, de Man TJB, Mandrekar JN, Schuetz AN, Jenkins S, Humphries R, Palavecino E, Vasoo S, Patel R. 2017. Multicenter Performance Assessment of Carba NP Test. J Clin Microbiol 55(6):1954-1960. doi: 10.1128/JCM.00244-17SSTAR: de Man TJB, Limbago BM. 2016. SSTAR, a stand-alone easy-to-use antimicrobial resistance gene predictor. mSphere 1(1): e00050-15. doi: 10.1128/mSphere.00050-15ARG-ANNOT database: Gupta SK, Padmanabhan BR, Diene SM, Lopez-Rojas R, Kempf M, Landraud L, Rolain J-M. 2014. ARG-ANNOT (Antibiotic Resistance Gene-ANNOTation), a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrobial Agents and Chemotherapy 58:212–220. doi: 10.1128/AAC.01310-13ResFinder database: Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, Aarestrup F, Larsen MV. 2012. Identification of acquired antimicrobial resistance genes. Journal of Antimicrobial Chemotherapy 67:2640–2644. doi: 10.1093/jac/dks261