MacVectorTip: Assembling Fungal Genomes using SPAdes

MacVector with Assembler can assemble bacterial genomes in just minutes on quite modest hardware. Currently MacVector has four de novo assembly tools (SPAdes, Velvet, Flye and Phrap).

But what of larger genomes? It is currently impractical to run de novo assemblies of Human genomes on a low cost Mac, though RNA-Seq analyses against the human transcriptome are possible. However, here we performed some complete genome de novo assembly tests on a sample NGS experiment from Aspergillus fischeri (NCBI SRA SRR10092049). This data set consists of 2x 18.2 million paired -end 150nt Illumina HiSeq reads, representing 5.5Gbp of sequence data. The assembly was run on a 2.9 GHz 6-core i9 MacBook Pro with 32 GB RAM, using SPAdes with 11 threads and slightly modified K-MER values.

As seen below, the complete assembly, including the optional Bowtie reference assembly step, took just over 28 hours in total. Maximum RAM usage during assembly was about 24 GB. 1,314 contigs were generated with a total combined length of 31.38 Mbp, right in line with the reported genome size with the longest contig 1,132,146 bp in length and an N50 Score of 350,491.

The information presented here gives you some idea of what is achievable on a modest machine using MacVector with Assembler. Assembly would be expected to be faster with a more restricted set of K-MER values, or on higher end machines such as the Mac Pro, Apple Studio or with much more RAM.


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