Sequence assembly

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Basic assembly

See how to assemble simple contigs and unitigs in Transform to sequences.

Differential assembly

MetaGraph allows for sequences to be assembled from a defined subgraph of an input annotated de Bruijn graph. In particular, a subset of labels may be defined as a foreground or in-group, while another may be defined as the background or out-group. From these, sequences can be assembled from a subgraph predominantly containing foreground k-mers and excluding background k-mers.

These subgraphs can be defined using a JSON configuration file. Examples are provided here and here.

Several differential assembly experiments may be defined for a single input annotated graph. These are organized into groups and experiments. A group is defined by a list of experiments and sets of foreground and background labels which are shared by these experiments. We recommend that labels with a substantially larger number of k-mers, such as reference genomes, are defined as shared. An experiment is defined by its own set of foreground and background labels, and by the assembly experiment parameters.

The assembly proceeds in four stages. In the first stage, the k-mers labeled with at least one of the foreground and background labels are enumerated to determine the initial subgraph. In the second stage, all labels associated with the subgraph unitigs are checked against the group’s shared label set, updating the foreground and background label counts accordingly. In the third stage, the foreground and background label counts, and assembly parameters, are used to determine which k-mers are filtered out from the subgraph. In the fourth stage, sequences are assembled from the subgraph constructed in stage three.

Differential assembly parameters

In the third stage of differential assembly, several parameters defined in the config JSON files are used to determine which k-mers from the initial subgraph are filtered out. A k-mer is considered to be an in-k-mer if it is annotated with in_min_fraction of the foreground labels (of the experiment plus the group’s shared labels). Analogously, a k-mer is considered to be an out-k-mer if it is annotated with more than out_max_fraction of the background labels. Next, the numbers of in- and out-k-mers are considered in each unitig of the initial subgraph. An entire unitig is discarded from the subgraph if less than unitig_in_min_fraction of its constituent k-mers are in-k-mers, if more than unitig_out_max_fraction of these k-mers are out-k-mers, or if more than unitig_other_max_fraction of the constituent k-mers contain other (non-in- or non-out-) labels.

Each sequence which is extracted from an experiment is labeled with the name defined for that experiment.