Note: This topic is not applicable to BAM-based projects.
The goal of sequence assembly is to generate a single contig for each contiguous segment of DNA represented in the sequence data set. Often you may obtain multiple contigs where you hoped for one, especially for larger projects where statistical fluctuations result in uneven coverage. SeqMan Pro provides several ways to build contigs into the arrangement that represents the original target DNA sequence:
•Associating contigs based on paired end data—this method can arrange the contigs into the correct order even when there are significant gaps in the data.
o You could then force-join the contigs at their termini by selecting Contig > Force Join Contigs. See Force Joining Contigs for detailed instructions.
o You may save the consensus sequences as a single contiguous sequence in the current order by selecting Contig > Save Consensus > As Single Sequence.
•Reassembling contigs—this method tests whether multiple contigs might assemble into a single contigs under alternative assembly parameters.
o Reducing Match size and/or Minimum match percentage Assembling parameter values may create conditions suitable for joining contigs, at the risk of introducing false joins.
o Reducing Gap and Gap length penalties may allow contig joining, but these values are less influential for this post-assembly process than for the core assembly alignment.
•Aligning contigs based on their consensus sequences—this method may be applied to determine whether multiple contigs may be joined after trimmed data are reintroduced into the project or using less stringent alignment parameters than were used for the initial assembly.