Because of the duplicated genome of salmonids, such stringent assembly criteria were necessary to reduce probabilities of assembling paralogous genes (Renaut et al. 2010).
The filtered SHS reads were assembled with Newbler version 2.6 (Roche Applied Science) using stringent assembly parameters (60 bases overlap and 95% overlap identity) and the '- rip' option that forces Newbler to place each read into one unique contig.
It is likely that the BACs not assembling into a respective contig is due to a small amount of overlap, stringent assembly conditions, or non-specific identification during DNA hybridization.
TASR uses a stringent targeted assembly scheme, where the more complex and unique a target sequence is, the less likely non-specific reads are to co-assemble, facilitating variant detection.
However, as mentioned above, due to the stringent criteria to assemble micSeqs (at least 50×) and lower coverage of NGS data from the 1 K genome project, most of micSeqs are short (average of 221 nt), and are likely to be only part of longer sequences in humans.
Expressed sequence tags were assembled with stringent parameters after processing with inbuild scripts, resulting in 37 138 contigs and 215 199 singlets.
A total of 45,474 high-quality ESTs with an average length of 471 bp were assembled with stringent Phrap parameters, yielding 12,161 contigs.
These BACs were assembled under stringent criteria that assured overlaps between BACs were ≥30 kb in size with ≥99.99% sequence identity.
Following stringent cleaning procedure, we assembled rice and sorghum cleaned EST and mRNA sequences using CAP3 with the following parameters: −p 95 –o 50 –g 3 –y 50 –t 1000 [ 27].
To minimize software-induced map inflation (Table 2), we collapsed the 1,546 'bPb' markers into 959 bins based on their segregation signatures concatenated across populations and used moderately stringent program settings to assemble a DArT skeleton bin map with JoinMap (LOD = 2; REC = 35).
