KMCP¶
KMCP uses genome coverage information by splitting the reference genomes into chunks and stores k-mers in a modified and optimized Compact Bit-Sliced Signature (COBS) index for fast alignment-free sequence searching. KMCP combines k-mer similarity and genome coverage information to reduce the false positive rate of k-mer-based taxonomic classification and profiling methods.
Profile Format¶
Taxpasta expects a tab-separated file with seventeen columns. This is generated with the kmcp profile
command. Taxpasta will interpret the columns as:
Column Header | Description |
---|---|
ref | |
percentage | |
coverage | optional |
score | |
chunksFrac | |
chunksRelDepth | |
chunksRelDepthStd | optional |
reads | |
ureads | |
hicureads | |
refsize | |
refname | optional |
taxid | |
rank | optional |
taxname | optional |
taxpath | optional |
taxpathsn | optional |
Please refer to the KMCP documentation for further description.