Kermit is a guided genome assembler using colored overlap graphs based on miniasm.
# Install kermit and minimap2 (requires zlib)
git clone --recursive https://github.com/rikuu/kermit && (cd kermit && make)
git clone https://github.com/lh3/minimap2 && (cd minimap2 && make)
# Color
minimap2/minimap2 -t8 -x map-pb reference.fa reads.fq > reference.paf
kermit/kermit-color reference.paf > reads.cf
# Overlap
minimap2/minimap2 -t8 -x ava-pb reads.fq reads.fq > reads.paf
# Layout
kermit/kermit -C reads.cf -f reads.fq reads.paf > reads.gfaKermit supports assembly guiding using either a reference genome or a genetic linkage map.
Kermit is heavily based on miniasm and as such shares most advantages and disadvantages with it. minimap2 is used to provide all-vs-all read self-mappings to kermit. Kermit outputs an assembly graph in GFA format.
The main difference is an added coloring step in the pipeline. Kermit uses minimap2 to map the reads to a reference genome (or draft assembly) and colors reads based on the mappings.
For now, only mapping given in PAF-format output by minimap and minimap2 is supported, i.e. no support for SAM/BAM is currently implemented.
For reference-guided assembly, coloring is done using reads mapped to a reference. Using genetic linkage maps is done by giving both the linkage map and the mappings to the reference the linkage map is relative to.
kermit/kermit-color reference.paf > reads.cf
kermit/kermit-color reference.paf map.txt > reads.cfA linkage map is given as tab-separated files with each line defining a marker by its position on a contig and a bin. lepmap3 gives applicable linkage maps and is recommended.
Both a simulated map for E. coli K-12 and a script for simulating linkage maps is included in misc folder.