Assemble the genome of HG002_NA24385_son using NextDenovo

  1. Download reads

wget ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/Ultralong_OxfordNanopore/guppy-V2.3.4_2019-06-26/ultra-long-ont.fastq.gz

  1. Prepare input file (input.fofn)

    ls ultra-long-ont.fastq.gz > input.fofn

  2. Prepare config file (run.cfg)

[General]
job_type = sge # here we use SGE to manage jobs
job_prefix = nextDenovo
task = all
rewrite = yes
deltmp = yes
parallel_jobs = 22
input_type = raw
read_type = ont # clr, ont, hifi
input_fofn = input.fofn
workdir = HG002_NA24385_son_assemble

[correct_option]
read_cutoff = 1k
genome_size = 3g # estimated genome size
sort_options = -m 50g -t 30
minimap2_options_raw = -t 8
pa_correction = 5
correction_options = -p 30

[assemble_option]
minimap2_options_cns = -t 8
nextgraph_options = -a 1

  1. Run

nohup nextDenovo run.cfg &

  1. Get result

  • Final corrected reads file (use the -b parameter to get more corrected reads):

    HG002_NA24385_son_assemble/02.cns_align/01.seed_cns.sh.work/seed_cns*/cns.fasta

  • Final assembly result:

    HG002_NA24385_son_assemble/03.ctg_graph/nd.asm.fasta

you can get some basic statistical information from file HG002_NA24385_son_assemble/03.ctg_graph/nd.asm.fasta.stat, the folowing is the assembly statistics with default parameters:

Type           Length (bp)            Count (#)
N10            168924870                   2
N20            127260938                   4
N30             94622851                   7
N40             85456034                  10
N50             79737202                  13
N60             69943198                  17
N70             58504138                  21
N80             40548231                  27
N90             19732879                  36

Min.               82439                   -
Max.           220056807                   -
Ave.            24389616                   -
Total         2877974703                 118

Note

This result will have some minor changes with the version upgrade.