comery / hifi-barcode-hiseq Goto Github PK

HIFIBarcode is used to produce full-length COI barcodes from pooled PCR amplicons generated by individual specimens.

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.

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.

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

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

• 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 

if you still use old versions, you can see PERL VERSION for help.

yangchentao at genomics dot cn
liushanlin at genomics dot cn
zhouchengran at genomics dot cn

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.

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.