Assembly of genomic reads of elite indica rice cultivar onto 2101 reference bacterial genomes for identification of co-sequenced endophytic bacteria.

Reference based assembly of genomic reads of the elite indica rice cultivar RP Bio-226 was carried out against 2101 reference bacterial genomes using Bowtie-2 genome assembly tool. Five types of data: Number of paired end reads concordantly aligned exactly only once, number of paired end reads concordantly aligned more than once, number of mates that make the pairs aligned exactly only once, number of mates that make the pairs aligned more than once and overall percentage of alignment were collected. Interpretation of the results and identification of endophytes based on these alignment statistics are described in detail in our research article "L.Battu, M.M. Reddy, B.S.Goud, K.Ulaganathan, K.Ulaganathan, Genome inside genome:NGS based identification and assembly of endophytic and genomes from rice genomic reads, Genomics (in press)".