HIFIBarcode
DESCRIPTION
HIFIBarcode is used to produce full-length COI barcodes from pooled PCR amplicons generated by individual specimens.
INSTALLATION
Pre-requisites
Operating system:
HIFIBarcode is designed to run on most platforms, including UNIX, Linux and MacOS/X. Microsoft Windows. We have tested on Linux and on MacOS/X, because these are the machines we develop on. HIFIBarcode is written in python language, and a version 3.5 or higher is required.
Published softwares involved:
VSEARCH v2.4.4. Rognes, Torbjørn, et al. "VSEARCH: a versatile open source tool for metagenomics." PeerJ 4 (2016): e258.
SOAPBarcode. Liu, Shanlin, et al. "SOAPBarcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons." Methods in Ecology and Evolution 4.12 (2013): 1142-1150.
Dependencies:
Make sure you have installed the fellowing modules or software before using HIFIBarcode.py
- Biopython version 1.5 or higher (required). Please check https://biopython.org/ and https://pypi.org/project/biopython/#description for more details on installation of biopython.
- Another python package - bold_identification is also required for getting complete function of HIFI-SE. See https://pypi.org/project/bold-identification/
- HIFIBarcode supposed you have installed the VSEARCH on your device, and its path in your $PATH. See https://github.com/torognes/vsearch
- HIFIBarcode needs software - barcode to achieve gap-filling procee, it can be found in same directory of HIFIBarcode.py
Here we go
download from the lastest release or just git clone
git clone https://github.com/comery/HIFI-barcode-hiseq.git
Type:
python3 HIFIBarcode.py -h
usage: HIFI-hiseq [-h] [-v]
{all,filter,assign,buildend,chain,gapfill,mkout,polish,taxonomy}
...
Description
An automatic pipeline for HIFI-hiseq project, including filtering
raw reads, assigning reads to samples, assembly HIFI barcodes
(COI sequences).
Version
2.1.0 2021-09-14 The latest version.
Author
yangchentao at genomics.cn, BGI.
zhouchengran at genomics.cn, BGI.
liushanlin at genomics.cn, BGI.
positional arguments:
{all,filter,assign,buildend,chain,gapfill,mkout,polish,taxonomy}
all run filter, assign, buildend, chain, and gapfill
filter filter raw reads by quality or expected_err
assign assign clean reads to samples
buildend buildends for each sample, output DNA fragment with tag
chain connect middle meta-paried reads to longer contigs
gapfill gap filling to generate raw contigs
mkout rename raw contigs to final COI barcodes
polish polish COI barcode assemblies, output confident barcodes
taxonomy do taxa identification on BOLD system
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
EXAMPLES
- step 1, run all
python3 HIFIBarcode.py all -outpre hifi -index 5 -q1 test1.fq.gz -q2 test2.fq.gz -primer indexed_primer.txt- step 2, run gap-filling
# at first, go to shell dir
cd hifi_gapfill/shell
# because this step will cost more memory, so I isolate this step.
# then, you can run all *.sh file in this fold by way you like.
# e.g. you can use qsub if you are a cluster user, or you can just
# run on your local computer.
ls *.sh|while read a; do qsub -cwd -l vf=1.5g $a;done
or:
sh *.sh
- step 3, generate output contigs
python3 HIFIBarcode.py mkout -outpre hifi -d hifi_gapfill- [optional] step 4, polish assemblies
python3 HIFIBarcode.py -outpre hifi -i hifi_barcodes.fa -index 5 PERL version
if you still use old versions, you can see PERL VERSION for help.
CONTACT US
yangchentao at genomics dot cn
liushanlin at genomics dot cn
zhouchengran at genomics dot cn
CITATION
Liu, Yang, Zhou, Zhou.(2017). Filling reference gaps via assembling DNA barcodes using high-throughput sequencing - moving toward to barcoding the world. Gigascience. 2017 Oct 25. doi: 10.1093/gigascience/gix104.
Copyright
This package is released under version 3 of the GNU General Public License (GPLv3). Please refer to https://www.gnu.org/licenses/gpl-3.0.html.