#Macvector assemble plasmid plus

Finally, click on the Velvet or SPAdes toolbar button to run the algorithms. You can also import compressed (gzip) files directly, with no need to uncompress them, saving a lot of disk space. Typically these are paired-end reads (either interleaved or as separate files), but they can be unpaired reads, consensus sequences exported from a different assembly, Ion Torrent, PacBio or Oxford Nanopore reads. SPAdes can often generate meaningful assemblies from relatively poor data where Velvet will fail without considerable tweaking of the parameters.īoth are invoked the same way: use File | New | Assembly Project to create a new project, then click on the Add Reads button and select the read files you want to import. With Velvet you often need to tweak the parameters for optimal performance, whereas SPAdes usually “just works”.

#Macvector assemble plasmid plus

Velvet is significantly the faster of the two, but SPAdes often generates longer contigs as it does a slightly better job at resolving repeats, plus it can handle many more data types for mixed read assemblies and has a smaller memory footprint, allowing it to be used for larger data sets.

Both are very capable assemblers with a small memory footprint. MacVector 16 incorporates two separate NGS de novo assemblers, Velvet and SPAdes. But with advances in the efficiency of algorithms and improvements in hardware, it is now possible to assemble quite large genomes on a Mac laptop. Not so long ago, you needed a powerful Linux server with lots of memory for de novo assembly of whole genomes. MacVector with Assembler contains some remarkably powerful algorithms for assembling Next Generation Sequencing (NGS) data.