Closing gaps in Assembly Projects and Align to Reference documents.

You can access many tools for closing the gaps in genome sequencing projects. If you select reads, then right click you will see a context sensitive menu with the following tools:

Export Consensus with/without Gaps
Align Selected Reads
Delete Selected Reads
Reset (unalign) Selected Reads
Export Selected Reads as FASTA/FASTQ
Select Matching Pairs – if you have aligned a set of paired-end reads, you can select individual read(s) and use this function to select the corresponding mate(s). This is particularly useful if you want to find pairs that will extend a contig and export them for further analysis/assembly.
Extend Reference with Selected Read - This is active if you have selected a single read that hangs over either end of a Reference sequence. This will extend the Reference in the appropriate direction using the sequence of the read.
Circularize Consensus - This is enabled if it detects direct repeats at the ends of a contig, and even tells you the length of the repeat it found. It will circularize the consensus and create a new circular sequence window with the repeat appropriately deleted.
Select Overlapping Reads Containing Selected Sequence - This is enabled if you select a short region in a read. All overlapping reads that contain that selected sequence will be selected. For paired reads you can then use Select Matching Pairs to select their mate, then Export Selected Reads as FASTQ/FASTA to export them to a file.

Not all tools are applicable or available in all editors. Plus some tools are only enabled when using paired end reads. Here's what's available in each editor.

Align to Reference editor

Export Consensus with/without Gaps
Align Selected Reads
Delete Selected Reads
Reset (unalign) Selected Reads
Export Selected Reads as FASTA/FASTQ
Select Matching Pairs
Extend Reference with Selected Read.
Select Overlapping Reads Containing Selected Sequence.

Reference Contig editor

Export Consensus with/without Gaps
Export Selected Reads as FASTA/FASTQ
Select Matching Pairs
Select Overlapping Reads Containing Selected Sequence.

De novo contig editor

Export Consensus with/without Gaps
Export Selected Reads as FASTA/FASTQ
Select Matching Pairs
Circularize Consensus

Closing gaps in Assembly Projects and Align to Reference documents.

Align to Reference editor

Reference Contig editor

De novo contig editor

Related Topics.