housed perl scripts for HIFI-barcode project
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HIFIBarcode.v1.3.pl
README.md

README.md

HIFIBarcode V1.3 (201805)

DESCRIPTION

HIFIBarcode is used to produce full-length COI barcodes from pooled PCR

amplicons generated by individual specimens.

INSTALLATION

tar -zxvf HIFIBarcode.v1.3.tar.gz

Source code

(1) Wrappper script:

HIFIBarcode.v1.3.pl: the wrapper script to run other Perl scripts to do the work you choose.

(2) Main scripts:

Seven Perl scripts in folder HIDIBarcode.V1.0/bin/, including:
- 1_split_extract.pl
- 2_uniqu_sort_cluster.Pro.pl
- 3_sep_extract_overlap.pl
- 4_cluster_fromend.pl
- 5_forgap_filling.pl
- 6_rename_kmer.pl
- 7_final.pl

(3) Published softwares:

VSEARCH v2.4.4. Rognes, Torbjørn, et al. "VSEARCH: a versatile open source tool for metagenomics." PeerJ 4 (2016): e258.   
COPE CMR v1.3. Liu, Binghang, et al. "COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly." Bioinformatics 28.22 (2012): 2870-2874.
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.

Pre-requisites

PERL v5

EXAMPLES

1: run wrapper script to get shell text and then sh runHIFIBarcode.sh to run HIFIBarcode
perl HIFIBarcode.v1.3.pl --fq1 test_1.fq --fq2 test_2.fq --index index_primer.txt --length 5 --cpunum 10 --outdir test --outpre testout sh test/runHIFIBarcode.sh

CONTACT US

Email:

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.

LATEST RELEASE

Version 1.3 201805

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.