Assembly & Annotation

Some of the tools in KBase available for Assembly and Annotation

KBase provides multiple Apps for de novo assembly of prokaryotic Next-Generation Sequencing (NGS) reads from various sequencing platforms. These assemblies can then be annotated to explore structural and functional features of a Genome or use it in other analyses. The interactive tutorials are a good way to learn about these workflows

Read Processing


De novo assembly of Illumina and Ion Torrent next-generation sequencing reads. Supports single-end and paired-end read libraries.

  • Assemble with HipMerHipMer is a highly-parallelized port of JGI’s Meraculous assembler. Meraculous is a de Bruijn graph-based which increases speed by not performing error correction. Instead, it bases contigs on already high-quality scores and fills the gaps based on localized assemblies from the reads. HipMer enhances the speed of Meraculous.

  • Assemble with IDBA-UDIDBA-UD is an iterative graph-based assembler for single-cell and standard short read data and is good for data of highly uneven sequencing depth. This assembler uses an iterative approach for selecting k-mer size that compensates for the information loss associated with single k-mer based de Bruijn graphs, making IDBA-UD one of the more accurate microbial assemblers.

  • Assemble with MaSuRCAMaSuRCA is a short read assembler that combines the benefits of de Bruijn graph and overlap layout consensus assembly approaches. The main concept is the creation of super-reads that contain sequence information present in the original reads, which super-reads are then extended in both directions using an efficient k-mer lookup table. MaSuRCA is one of a smaller set of assemblers biologists use for eukaryotic assembly.

  • Assemble with MEGAHITMEGAHIT is a single node assembler for large and complex metagenomics NGS reads. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly, making it fast and especially suitable for assembly of small metagenomes, metatranscriptomes or low-coverage data in general.

  • Assemble with SPAdesSPAdes is a single-cell and standard assembler based on paired de Bruijn graphs, considered to be one of the most accurate microbial assemblers. SPAdes employs a multisized de Bruijn graph which detects and removes bubble and chimeric reads, estimates insert distance from paired kmers, and computes contigs based on paired assembly graph.

  • Assemble with VelvetVelvet is a classic de Bruijn graph based assembler that works by efficiently manipulating de Bruijn graphs through simplification and compression. It eliminates errors and resolves repeats by first using an error correction algorithm that merges sequences together. Repeats are then removed from the sequence via the repeat solver that separates paths which share local overlaps.

  • Compare assemblies with QUAST – Assess the output assemblies from different configurations of the same assembler, or compare assemblies from multiple assemblers to determine which one is optimal for downstream analysis.


Genomes can be annotated with Prokka or RAST.

The output of the annotation apps is a Genome, which is displayed in a tabular genome viewer (see below) that shows information about the Genome as well as a list of contigs and the genes that were called on each contig.

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