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Protocol publication

[…] Bowtie2 (). The MC2 155 draft genome sequence was assembled using the M. smegmatis (NC_008596) strain as the template, while the 4XR1 and 4XR2 sequences were assembled by using the MC2 155 strain. The draft genomes of MC2 155, 4XR1, and 4XR2 were 6,988,269 bp (6,790 genes, 6,625 coding sequences [CDS] and 54 RNAs [47 tRNA, 6 rRNA, and 1 ncRNA]), 6,988,337 bp, and 6,988,302 bp (6,791 genes) long, respectively, with a GC content of 67.4%. The genomes were annotated using Rapid Annotation Transfer Tool (RATT) (), with annotation from NC_008596 being transferred to MC2 155 and the annotations of MC2 155 transferred to 4XR1 and 4XR2., The preprocessing of the assembled genome was performed using Picard tools (v1.119), while variant calling was performed using Genome Analysis Toolkit (GATK) (v3.1-1) (). The GATK-prescribed best practices were followed to filter and accept single nucleotide polymorphisms (SNPs) and insertion and deletions (indels). The SNP and indel annotations for the strains were added using snpEff (). A total of 133 indels and 90 SNPs were observed in MC2 155. The 4XR1 strain showed 19 indels and 2 SNPs, while the 4XR2 strain showed 14 indels and 2 SNPs., The genome sequences of these strains will be useful for obtaining a global understanding of the mechanism of drug resistance and also providing new insights into the biology of M. smegmatis, which can also be extrapolated to M. tuberculosis and may pave the way for exploring different treatment strategies., The draft genome sequences of MC2 155, 4XR1, and 4XR2 have been deposited at DDBJ/EMBL/GenBank under the accession numbers CP009494 (strain MC2 155), CP009495 (strain INHR1), and CP009496 (strain INHR2)., Citation Mohan A, […]

Pipeline specifications

Software tools Picard, GATK, SnpEff