How to run the Add reads to contigs

        Toolbox | Genome Finishing Module (Image finishing_tools_folder) | Add reads to contigs (Image add_reads_to_contigs_16_n_p)

This opens the dialog shown in figure 6.2.

Image add_reads_to_contig_step1
Figure 6.2: Select sequence reads.

Select sequence reads and click Next. This opens the dialog shown in figure 6.3.

Image add_reads_to_contig_step2
Figure 6.3: Select a contig.

Select the contig or the list of contigs that you want to add by clicking on the folder (Image find_in_project). Next, set the mapping options (figure 6.4).

Image add_reads_to_contig_step3
Figure 6.4: Set mapping options.

Read alignment
  • Mismatch cost. The cost of a mismatch between the read and the reference sequence. Ambiguous nucleotides such as "N", "R" or "Y" in read or reference sequences are treated as a mismatches and any column with one of these symbols will therefore be penalized with the mismatch cost.
  • Linear gap cost. The cost of a gap is computed directly from the length of the gap and the insertion or deletion cost. This model often favors small, fragmented gaps over long contiguous gaps.
    • Insertion cost. Can be set at 1, 2, or 3.
    • Deletion cost. Can be set at 1, 2, or 3.
  • Affine gap cost. An extra cost associated with opening a gap is introduced such that long contiguous gaps are favored over short gaps.
    • Insertion open cost. Cost of opening an insertion in the read (a gap in the reference sequence).
    • Insertion extend cost. Cost of extending an insertion in the read (a gap in the reference sequence) by one column.
    • Deletion open cost. Cost of a opening a deletion in the read (gap in the read sequence).
    • Deletion extend cost. Cost of extending a deletion in the read (gap in the read sequence) by one column.

  • Length fraction. Minimum length fraction of a read that must match the reference sequence.
  • Similarity fraction. Minimum fraction of similarity between read and reference sequence.
  • Auto-detect paired distances. Determine the insert size of paired data sets.
  • Global alignment. If selected, end gaps are treated as mismatches. If not checked, end gaps have no cost. Auto-detect paired distances is only accessible when using the relevant data sets.
Non-specific match handling
  • Map randomly. Reads with more than one match are assigned randomly.
  • Ignore. Reads with more than one match are ignored.

After clicking Finish in the Result handling step, the reads will be added to the existing mapping of reads to contigs.