Sequence search¶
Attention
This page is in development
MetaGraph allows for query sequences to be searched against the graph alone, returning the closest path in the graph, or against the annotated graph, returning a set of associated labels. These are referred to as the align and query regimes, respectively.
Align sequences to the graph¶
Sequence alignment features can be accessed via metagraph align.
By default, a sequence of graph paths is output which form a disjoint cover of the
query sequence. Depending on the desired level of sensitivity, alignment options range
from simply finding exact k-mer matches to performing an alignment to finding a
best-scoring path in the graph.
Exact k-mer matching¶
Also referred to as pseudo-alignment, this feature is accessed via the additional --map flag.
This mode extracts the sequence of k-mers from a query sequence and reports the indices
of the corresponding nodes in the graph. An example command may be:
metagraph align --map -i MYGRAPH.dbg MYREADS.fa
Input sequences may be in FASTA or FASTQ format (uncompressed or gzipped).
The output is in TSV format with the first column being an input k-mer and the second
column being the corresponding node in the graph (or 0 if not present).
For less verbose output, the additional --query-presence and --count-kmers
flags are available.
--query-presenceoutputs one line per sequence indicating whether the sequence is present (1) or absent (0). A sequence is considered to be present if its fraction of present k-mers is at leastd, as set by the--discovery-fractionflag.--count-kmersoutputs one line per sequence in TSV format. The first column is the sequence header, while the second column is of the forma/b/c, whereais the number of matching k-mers,bis the total number of k-mers, andcis the total number of unique matching k-mers (where reverse complements are considered to be matching).
Sequence-to-graph alignment¶
Additional parameters¶
Query sequences against the index¶
(Experiment discovery)