Variant Discovery Tools

« Polymorphism Analyses in Light Of MAssive dna sequencing » (PALOMA) platform is designed for Evolution projects.

Evolution projects rely on the Next Generation Sequencing (NGS) technologies to try to decipher the dynamics of genomic changes as well as the molecular bases and the mechanisms underlying adaptative evolution of micro-organisms.
To address these problematics, we designed a bioinformatic pipeline, called SNiPer, which allows the comparison and the detection of small variations (SNPs and InDels) between sequencing reads of evolved clones and the genomic reference sequence of their ancestor. Based on the SSAHA2 and SSAHAsnp packages, SNiPer takes into account raw sequencing data and associated qualities to discriminate between true variations and sequencing errors.
This functionality offers different tools to explore and analyze the mutations predicted by SNiPer in their genomic and functional context.
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