JTK is a regional 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

If it is not up to date, please rustup update so that the version would be more 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

Move ./target/release/jtk at the location you want.

0. Prepare the reads to be assembled.
   • Align your reads to the reference and index the bam file by minimap2 For example, minimap2 -x map-ont -t $THREADS --secondary=no -a $REFERENCE $READS | samtools sort -@$THREADS -OBAM > aln.bam && samtools index aln.bam.
   • Use bash ./script/extract_region.sh $REFERENCE $BAM $REGION > reads.fastq, where $REGION should be a region specification, such as chr1:10000000-15000000.
   • It is the same as samtools view -OBAM $BAM $REGION | samtools fastq > reads.fastq
   • A region should be smaller than 10Mbp and should not end with a segmental duplication (TODO: this should be fixed).
1. Modify example.toml as you want.
   • See example.toml for the explanation of the parameters.
   • I recommend to use absolute path for the input and the output directory.
   • JTK would create the temporary file at the current directory. Please exec at the location where you have a write permission.
   • sed is useful. For example, cat example.toml | sed -e "/^input_file/c input_file = \""$DATA"\"" ... > profile.toml would replace the input file with $DATA.
2. Run jtk pipeline -p example.toml
   • Several JSON files and assmbly graphs would be created.
   • In addition, prefix.sam is the alignment between the reads and the assembly, and prefix.coverage.tsv is the coverage track on the assembly.

Also, there is an agnostic subcommend, jtk stats -f out.stat $JSON_FILE > /dev/null and out.stat contains some useful information. (Caution: This command pipes the input file to the stdout. So do not forget to redirect it to the /dev/null.)

minimap2 --version # Should be larger than 2.23 
jtk --version # Should be larger 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 # This commend uses 20 threads.

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

Please do not input reads comming from a region more than 10M bp long. It has not been tested.

Contact: Bansho Masutani [email protected]