Haplotyping
Project description
haplotyping
Indexation process
See haplotyping.index for more details
graph TD;
fastq["<b>READS</b><br/>fastq files"];
detect["detect splitting k-mer in reads"];
direct["store direct connections reads"];
fastq --> kmc;
kmerlist --> splitlist;
fastq --> detect;
subgraph KMC Software
k["k-mer<br/>size"]
minfreq["minimum<br/>k-mer frequency"]
maxfreq["maximum<br/>k-mer frequency"]
kmc(<b>kmc database</b>)
k.->kmc
minfreq.->kmc
maxfreq.->kmc
end
subgraph scripts
kmcanalysis["<i>kmc_analysis</i>"]
kmerlist["<b>k-mer list</b>"]
kmcanalysis-->sort
sort-->gzip
gzip-->kmerlist
kmc-->kmcanalysis
end
subgraph HDF5 Database
splits["splitting k-mers"]
bases["splitting bases"]
direct["direct connections"]
partitioning["partitioning"]
indirect["indirect connections"]
splits-.->partitioning
partitioning-.->indirect
end
subgraph haplotyping.index
subgraph Splits
splitlist["get splitting k-mers and<br/>bases from sorted list"]
automaton["automaton<br/>splitting k-mers"]
splitlist-->automaton
splitlist--"storage"-->splits
splitlist--"storage"-->bases
end
subgraph Connections
detect["detect splitting k-mer in reads"]
partition["partition the graph"]
read["sort indirect connections reads"]
automaton-->detect
detect--"optional"-->partition
partition --> read
detect--"storage"-->direct
partition--"storage"-->partitioning
read--"storage"-->indirect
end
end
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