Compare · 3 tools
Genome assembly and quality tools you can run online
These tools construct genome sequences from raw reads, bin metagenomic contigs into microbial genomes, and evaluate assembly completeness using conserved orthologues.
What genome assembly and quality tools do
Genome assembly reconstructs continuous sequences from sequencing reads or fragments. Depending on the experimental setup, this involves assembling raw short and long reads into contiguous sequences or clustering contigs from mixed microbial communities into individual genome bins using sequence composition and cross-sample coverage.
Following assembly, assessing sequence quality is necessary. This evaluation extends beyond structural continuity metrics such as N50 by examining whether expected biological sequence elements, such as universal single-copy orthologues, are present in the final sequence sets.
Compared
- BUSCOGenome assembly and qualityAssesses completeness of genome assemblies, gene sets, and transcriptomes using universal single-copy orthologs.See its pageAs a job
- MaSuRCAGenome assembly and qualityAssembles genomes from short Illumina reads, alone or combined with long reads, using super-reads.See its pageAs a job
- MetaCATMetagenomicsBins metagenome assemblies into genomes using coverage and composition, and links them with host traits.See its pageOn demand
How to choose
For de novo genome assembly from sequencing reads, MaSuRCA constructs assemblies from Illumina paired-end reads, either on their own or alongside long reads from PacBio or Oxford Nanopore. It collapses short reads into super-reads and can use short-read data to error-correct long reads into mega-reads. In contrast, MetaCAT does not perform read-level assembly; it operates downstream on assembled metagenomic contigs and alignment files, clustering contigs into microbial genomes using coverage profiles and sequence composition.
BUSCO serves a distinct role focused on quality assessment rather than assembly or binning. Once MaSuRCA has generated an assembly or MetaCAT has grouped contigs into genome bins, BUSCO evaluates the completeness of the genome assemblies, transcriptomes, or gene sets against lineage-specific, single-copy orthologue datasets derived from OrthoDB.
Input requirements and computing environments also separate these tools. MaSuRCA runs exclusively on Linux and mandates at least 50x coverage of Illumina paired-end reads before long reads can be added, requiring high computational capacity such as 2 terabytes of RAM for a 30 Gb plant genome. MetaCAT operates on x86_64 Linux and arm macOS, supports GPU acceleration with CuPy, and requires external reference databases for CheckM2 and GTDB-Tk. BUSCO manages the automatic download of lineage datasets across eukaryota, prokaryota, and viruses, running pipelines through Miniprot, Metaeuk, or Augustus, though it requires dependency verification if installed without containers or package managers.
Questions
Can I run these tools without a GPU or installing anything?
Yes. The research agent runs each of these on a machine of its own — some are preinstalled, others are set up the first time a task needs them — and reads the results back to you.
Can MaSuRCA assemble genomes using only long reads?
No. MaSuRCA requires Illumina paired-end reads as an essential prerequisite for all workflows, requiring at least 50x coverage of Illumina reads before PacBio or Oxford Nanopore data can be integrated.
How does BUSCO assess genome quality compared to N50?
While N50 assesses assembly continuity based on sequence length, BUSCO assesses biologically informed completeness by checking whether expected single-copy orthologues are present, duplicated, fragmented, or missing.
What input data does MetaCAT require?
MetaCAT requires assembled metagenomic contigs and alignment BAM files across samples to calculate contig coverage and sequence composition.
Which execution pipelines are supported by BUSCO?
BUSCO supports Miniprot, Metaeuk, and Augustus pipelines to identify candidate orthologues across eukaryotic, prokaryotic, and viral lineages.
Written from each tool's own documentation, as summarised on its page here. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.