This Documentation provides some tips for running Nanopore Pore C pipeline

• Required input files:

  a) a merged fastq file for each sample

  b) raw fast5 files stored in one directory for each sample

  c) a sequencing_summary text file for each sample

  d) reference genome fasta file. The "GRCh38.fasta.gz" file provided by the original pipeline is NOT a real fasta file.

• To run on cluster

  a) the correct conda environment name is : conda activate pore-c-snakemake, NOT pore_c_snakemake as shown in the original repo.

  b) allow more than 4G memory for running snakemake, otherwise some conda environment installation may fail.

  c) log files are stored at: results/logs/results/

  d) the workflow "pairs" and "cooler" are not included in the workflow "all". You need to run them additionally.

• Output

  a) I don't see any of the below output files were generated as described in the original repo, with or withour phased vcf file:

  matrix/

  pairs/

  assembly/

  juicebox/

  b) a extra step is needed to merged all splited bam files

  c) the DNA contact information is stored in the file: merged_contacts/*.concatemers.parquet. Convert it to the csv format if needed.