seqGraph

SEQ is a conjugated assembly algorithm that constructs a conjugate map according to Barcode connection information between Contig, and finds the most likely connection relationship between Contig.

Requirement

htslib

Install

git clone https://github.com/panguangze/seqGraph
mkdir build
cd build
cmake .. && make

Running

make input

Add tgs data into assembly process
p_tgs -b tgs.bam -c contig.fasta -o out.fasta

tgs.bam aligned the tgs reads to the assemblied raw contigs.

overlap_end input.bam graph.txt 500,

The input.bam is aligned NGS reads to the contigs. The last parameters is the end length of contig for barcode statistic

seqGraph \
    -g  graph.txt\ // graph input
    -o  assembly_orders.txt\ //assemly contigs order and orientations
    -i  1 //iteration times, more iteration times longer scaf length but less accuracy

make fasta from assembly result

python scripts/make_fa.py assembly_orders.txt out.fasta