Puzzler Large Materials

Large file archive for Puzzler genome assembly pipeline v1.9. Note that the Apptainer container puzzler_v1.8.sif only contains the dependencies required, and those dependencies work for puzzler v1.9. To use Apptainer, fill out the samples.tsv with your runtime ("Apptainer"), the path to the .sif, and all your files. Note that there is also a fully contained Conda environment including the puzzler binary and all dependencies: https://anaconda.org/channels/heritabilities/packages/puzzler/overview Link to Github repository for the software here: https://github.com/merondun/puzzler The Fungus dataset (Fungus.HiFi.fastq.gz, *HiC.fastq.gz) consists of a small subset of reads from this project's genome assembly (100,000 HiFi reads and 10 million paired-end Hi-C reads), selected to enable rapid assembly testing (takes around 40 minutes with 16 cores and 64Gb RAM using --no_juice). The pipeline puzzler can be run with these files using puzzler -s Fungus -m samples.tsv, ensuring that you modify the paths to the working directory, container .sif, fastq.gz, and .fna. The large MP4 file shows Juicebox manual curation for the 11 benchmarked genomes, also archived on Youtube.