General musings from the MacVector team about sequence analysis, molecular biology, the Mac in general and of course your favorite sequence analysis app for the Mac!

Automated algorithms can only take you so far with genome assembly. The final steps involved in finishing a genome always need manual intervention. MacVector’s various assembly editors have many tools for helping finish genome sequencing projects. For example, closing gaps, extending reference sequences and even automatically circularizing contigs. If you select reads, then right click (or use CTRL-left 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

Read more about the various assembly tools in MacVector.

Simple DNA sequence assembly on a Mac with MacVector with Assembler.

MacVector has a software plugin called Assembler that integrates directly into the DNA sequence analysis toolkit and provides DNA sequence assembly functionality. Dealing with sequencing reads has never been easier.

MacVector includes no less than five different assemblers just a few mouse clicks away from your sequencing reads. Phrap assembles Sanger sequencing reads or existing contigs, while there are three separate NGS de novo assemblers – Velvet for short read datasets, Flye for Nanopore and PacBio long reads and SPAdes for mixed assemblies. For reference assembly Bowtie2 can map millions of sequencing reads against genomic reference sequences and is ideal for RNASeq gene expression analysis data too.

Assembler is tightly integrated into MacVector. It’s easy to bring sequencing reads into MacVector, and it’s just as easy to directly design primers for a contig, run BLAST searches on a contig, and much more, right from your desktop!