Fast and accurate de novo assembler for third generation sequencing (TGS) long reads. To polish raw contigs generated by third generation sequencing (TGS) long reads, please use NextPolish.
NextDenovo includes two parts:
NextCorrect (Binary released)
This package aims to correct the TGS long reads with approximately 15% sequencing errors. The design philosophy is from Falcon. After correction, for nanopore data, the identity is about 97-98%, most of remaining errors are located in the homopolymer or tandem repeat regions.NextGraph (Releasing soon)
This package aims to construct the string graph with corrected data.
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REQUIREMENT
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DOWNLOAD
click here or use the following command:
wget https://github.com/Nextomics/NextDenovo/releases/download/v1.1.1/NextDenovo.tgz -
INSTALL
cd NextDenovo && make -
UNINSTALL
cd NextDenovo && make clean -
RUN
nextDenovo test_data/run.cfg -l log.txt -
INPUT
[General] # global options
job_type = sge # [local, sge, pbs...]. (default: sge)
job_prefix = nextDenovo # prefix tag for jobs. (default: nextDenovo)
task = all # task need to run [all, correct or graph]. (default: all)
rewrite = no # overwrite existed directory [yes, no]. (default: no)
deltmp = yes # delete intermediate results. (default: yes)
rerun = 3 # re-run unfinished jobs untill finished or reached ${rerun} loops, 0=no. (default: 3)
input_type = raw # input reads type [raw, corrected]. (default: raw)
input_fofn = input.fofn # input file, one line one file. (required)
workdir = 01.workdir # work directory. (default: ./)
usetempdir = /tmp/test # temporary directory in compute nodes to avoid high IO wait. (default: no)
nodelist = avanode.list.fofn
# a list of hostnames of available nodes, one node one line, used with usetempdir for non-sge job_type.
cluster_options = -l vf={vf} -q all.q -pe smp {cpu} -S {bash} -w n
# a template to define the resource requirements for each job, which will pass to DRMAA as the nativeSpecification field.
[correct_option] # options using only in corrected step.
read_cuoff = 1k # filter reads with length < read_cuoff. (default: 1k)
seed_cutoff = 25k # minimum seed length. (required)
seed_cutfiles = 10 # split seed reads into ${seed_cutfiles} subfiles. (default: ${pa_correction})
blocksize = 10g # block size for parallel running. (default: 10g)
pa_raw_align = 10 # number of alignment tasks used to run in parallel. (default: 10)
pa_correction = 15 # number of corrected tasks used to run in parallel. (default: 15)
minimap2_options = -x ava-ont -t 10
# minimap2 options, used to set PacBio/Nanopore read overlap. (required)
sort_options = -m 5g -t 2 -k 50
# -t, number of threads to use. (defalut: 8)
# -m, set maximum available buffer size, larger buffer size will accelerate sort process, suffix K/M/G. (defalut: 40G)
# -k, maximum depth of each overlap, larger depth will produce more accurate and more corrected data with slower speed. (defalut: 40)
correction_options = -p 10
# -p , --process, set the number of processes used for correcting. (default: 10)
# -s, --split, split the corrected seed with un-corrected regions. (default: False)
# -fast, 0.5-1 times faster mode with a little lower accuracy. (default: False)
# -max_lq_length, maximum length of a continuous low quality region in a corrected seed, larger max_lq_length will produce more corrected data with lower accuracy. (default: auto [pb/1k, ont/10k])
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OUTPUT
cns.fasta with fasta format, the fasta header includes primary seqID, length, approximate corrected bases percentage (%). The two flanking un-corrected sequences are trimed. -
HELP
Please raise an issue at the issue page. -
Contact information
For additional help, please send an email to huj_at_grandomics_dot_com. -
COPYRIGHT
NextDenovo is freely available for academic use and other non-commercial use. For commercial use, please contact NextOmics. -
PLEASE STAR AND THANKS
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FAQ
- Which job scheduling systems are supported by NextDenovo?
NextDenovo use DRMAA to submit, control, and monitor jobs, so in theory, support all DRMAA-compliant system, such as LOCAL, SGE, PBS, SLURM. - How to continue running unfinished tasks?
No need to make any changes, simply run the same command again. - How to reduce the total number of subtasks?
Please increase blocksize and reduce seed_cutfiles. - How to speed up NextDenovo?
Currently, the bottlenecks of NextDenovo are minimap2 and IO. For minimap2, please see here to accelerate minimap2, besides, you can increase -l to reduce result size and disk consumption. For IO, you can check how many activated subtasks using top/htop, in theory, it should be equal to the -p parameter defined in correction_options. Use usetempdir will reduce IO wait, especially if usetempdir is on a SSD driver. - How to specify the queue name/cpu/memory/bash to submit jobs?
Please use cluster_options, NextDenovo will replace {vf}, {cpu}, {bash} with specific values needed for each jobs. - RuntimeError: Could not find drmaa library. Please specify its full path using the environment variable DRMAA_LIBRARY_PATH.
Please setup the environment variable: DRMAA_LIBRARY_PATH, see here for more details. - ERROR: drmaa.errors.DeniedByDrmException: code 17: error: no suitable queues.
This is usually caused by a wrong setting of cluster_options, please check cluster_options first. If you use SGE, you also can add '-w n' to cluster_options, it will switch off validation for invalid resource requests. Please add a similar option for other job scheduling systems.
- Which job scheduling systems are supported by NextDenovo?