discoSnp++

[…] WB, DH_A, and GS_B, using BLASTn megablast, with the same parameters as described above, and reads which hit only the majority assemblages were removed. The remaining reads were then included in the discoSNP analysis as below.Single nucleotide variant (SNV) calling was performed by entering trimmed reads into discoSNP v2.1.2 () with parameters -c 4 –b 1 –k 31 –P 3, and a separate run for each ass […]

[…] Robust SNPs (highly or very highly designable for genotyping assay designs) polymorphic between the ‘Baccara’ and ‘PI180693’ parental lines were inferred using the kissreads module of the discoSnp tool [] on cleaned reads generated by sequencing the 48 ‘Baccara’ x ‘PI180693’ RILs. Kissreads provides the coverage for each SNP on reads for each RIL. Considering that less sequence data wa […]

[…] may be wrong (with a controlled percentage).Thus, the bloom filter representation has the main advantage of a very low memory footprint. For instance, nearly 3 billion reads (100 bp) were analyzed by DISCOSNP, using at most 5.7 GB of memory. Moreover, the low memory footprint does not imply a degradation in the running time. The COMMET tool, being a heuristic based only on a bloom filter, is also […]

[…] d to be 3.7 × sd and 5.9 × sd lower than the average, respectively. This shows that less (if any) SNPs are detected in these regions because their high variability prevents the identification of what discoSNP names a SNP: a region of 61 consecutive residues among which only the central base differs between the two strains. What lacks in these highly variable regions is not the differing base, but […]