Saving Assembly Projects

You can save an assembly project so that you can work on it at a later date, or you can save any contig consensus sequence as a single MacVector sequence.

SAVING the ASSEMBLY PROJECT

With the assembly project window active, choose "Save" or "Save As..." from the "Edit" menu. Type or select a file name then click "Save" to save the assembly. MacVector uses a File Package to store the individual files of the Assembly Project. The actual project is saved as a BSML file, an XML-based format. This file will also contain and trace files. However, any file based reference will not be stored within this file. Also note that the individual BAM files and BAM file indexes are also stored within the File Package. Right click and choose Show Contents to view the individual files.

SAVING a CONSENSUS SEQUENCE

Make sure you have a contig editor window active, then choose "Save As..." from the "Edit" menu. The only format option will be "MacVector Single Nucleic Acid Sequence". This will save the consensus sequence into a standard MacVector format file. Although the actual residues of the assembled sample sequences are not included in the file, their names and locations are saved as "Read" features as a reminder of the files you used to create the assembly.

Exporting Contigs

The FILE | EXPORT AS.. menu option allows contigs and consensus sequences to be exported in ASSEMBLY PROJECT, FASTA or FASTQ formats.

Note that if the output format is ASSEMBLY PROJECT then any selection is ignored and the entire project is exported into a new file. The following steps apply only to FASTQ/FASTA output files.

• From the Project window:
  • If no selection is made then every item in the project is saved to a new file.
  • If a reference or de novo contig is selected it will save a file containing all its child contigs, all mapped reads and no reference contig sequence or reference contig consensus. If no child contigs were generated, then no child contigs will be included.
  • If any reference or de novo contig is selected, then unselected contigs are ignored.
  • The selection of child contigs is ignored.
  • From an expanded Reference contig and the unassembled reads file selected, it will save a file containing all unaligned reads and no other sequences.
• From an open Reference Contig
  • it will save a file containing the reference sequence and the consensus.
  • If you have any selected reads in an open reference/de novo Contig it will save those reads.
  • You can choose FILE | EXPORT CONSENSUS AS... to export the consensus with or without gaps.
• From an open Child Contig
  • it will export a single sequence file with the consensus sequence.
• From an open de novo Contig
  • it will export a single sequence file with the consensus sequence.
  • You can choose FILE | EXPORT CONSENSUS AS... . to export the consensus with or without gaps.

Additionally from the Closing Gaps tools, you can export selected reads.

Related Topics.

Closing Gaps in Assemblies

Align to Reference

Assembler

Importing Fastq data

Bowtie

Phrap