MinION Nanopore for sequence assembly and read mapping¶

usage: MinION_mapping.py [-h] [-j JID] -o OUTPUT_LABEL -fa REF_FA -fq
                         FASTQ_FILE
                         [--ngmlr_addon_parameters NGMLR_ADDON_PARAMETERS]
                         [--wtdbg2_addon_parameters WTDBG2_ADDON_PARAMETERS]
                         [--wtpoa_cns_addon_parameters WTPOA_CNS_ADDON_PARAMETERS]
                         [-m MEM] [-k KMER] [-s GENOME_SIZE]

optional arguments:
  -h, --help            show this help message and exit
  -j JID, --jid JID     enter a job ID, which is used to make a new directory.
                        Every output will be moved into this folder. (default:
                        MinION_mapping_yli11_2020-09-02)
  -o OUTPUT_LABEL, --output_label OUTPUT_LABEL
                        output_label (default: None)
  -fa REF_FA, --ref_fa REF_FA
                        reference fa (default: None)
  -fq FASTQ_FILE, --fastq_file FASTQ_FILE
                        MinION fastq file (default: None)
  --ngmlr_addon_parameters NGMLR_ADDON_PARAMETERS
                        MinION fastq file (default: None)
  --wtdbg2_addon_parameters WTDBG2_ADDON_PARAMETERS
                        MinION fastq file (default: None)
  --wtpoa_cns_addon_parameters WTPOA_CNS_ADDON_PARAMETERS
                        MinION fastq file (default: None)
  -m MEM, --mem MEM     required mem in MB (default: 15000)
  -k KMER, --kmer KMER  kmer size (default: 13)
  -s GENOME_SIZE, --genome_size GENOME_SIZE
                        Approximate genome size (k/m/g suffix allowed)
                        (default: 0)

Summary¶

This pipeline performs sequence assembly using wtdbg2 as well as read mapping using ngmlr

If no -fa is specified, only sequence assembly will be performed.

https://github.com/ruanjue/wtdbg2

https://github.com/philres/ngmlr

Input¶

Fastq file from Nanopore -fq
Output label -o
Optional, a reference fasta sequence to perform read alignment -fa

Usage¶

hpcf_interactive

module load python/2.7.13

MinION_mapping.py -fa Townes_build2.fa -fq all.fq.gz -o test

Output¶

Results are provided in the jid folder.

*.ctg.fa assembled contig.

*.fix.st.bam read mapping bam file.

Comments¶

code @ github.