JTK is a targeted diploid genome assembler.

• minimap2 with version >= 2.23.
• Rust with version >= 1.66.0 nightly.

First, check the version of the Rust language.

cargo --version

The minimum required version is 1.66.0-nightly (otherwise, rustup update so that the version is greater than or equal to 1.66.0-nightly). Then,

git clone https://github.com/ban-m/jtk.git
cd jtk
cargo build --release
./target/release/jtk --version 
minimap2 --verion # minimap2 is needed.

Move ./target/release/jtk to the location in $PATH.

Suppose we have the following variables --

• REFERENCE: a reference sequence in FASTA format.
• READS: reads in FASTA format (recommended: ONT reads)
• REGION: target region in [CHR]:[start]-[end] format (e.g., chr1:10000000-15000000). This region should be smaller than 10Mbp and should not end/starts in a segmental duplication.

0. Prepare the reads for assembly.
   • Map your reads to the reference and index the bam file with minimap2:

   minimap2 -x map-ont -t $THREADS --secondary=no -a $REFERENCE $READS |\
      samtools sort -@$THREADS -OBAM > aln.bam && samtools index aln.bam
   

   • bash ./script/extract_region.sh $REFERENCE $BAM $REGION > reads.fastq
     This is equivalent to samtools view -OBAM $BAM $REGION | samtools fastq > reads.fastq.
1. Modify example.toml
   • See example.toml for an explanation of the parameters.
   • I recommend using absolute paths for the input and the output directory.
   • JTK would create the temporary file at the current directory. Please exec at the location where you have a write permission.
   • sed is useful. For example, cat example.toml | sed -e "/^input_file/c input_file = \""$DATA"\"" ... > profile.toml would replace the input file with $DATA.
2. Run jtk pipeline -p example.toml
   • This would create several JSON files and assmbly graphs.
   • In addition, prefix.sam is the alignment between the reads and the assembly, and prefix.coverage.tsv is the coverage trace on the assembly.

minimap2 --version # Should be greater than 2.23 
jtk --version # Should be greater than 0.1
wget https://mlab.cb.k.u-tokyo.ac.jp/~ban-m/jtk/COX_PGF.fastq.gz
gunzip COX_PGF.fastq.gz
wget https://mlab.cb.k.u-tokyo.ac.jp/~ban-m/jtk/COX_PGF.toml
jtk pipeline -p COX_PGF.toml 2> log

Then, the assembly graph is available at cox_pgf/temp.gfa.

Please do not enter reads coming from a region longer than 10M bp long. It has not been tested.

Contact: Bansho Masutani [email protected]