At present, some people have posted articles about the analysis process of WGD. I searched for the keyword "wgd pipeline" and found the following:

GenoDup: https:// github.com/MaoYafei/GenoDup-Pipeline
https://peerj.com/articles/6303/
WGDdetector: https:// github.com/yongzhiyang2 012/WGDdetector
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2670-3
wgd: https:// github.com/arzwa/wgd
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1142-2#Sec1
https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-017-0399-x
GeNoGAP https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1142-2
https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-017-0399-x
https://github.com/dfguan/purge_dups
https://www.biorxiv.org/content/10.1101/2020.01.24.917997v1

This article introduces the usage of wgd.

Wgd cannot be installed directly with bioconda at present, so it is a little troublesome to install, because it depends on a lot of software. wgd depends on the following software

BLAST
MCL
MUSCLE/MAFFT/PRANK
PAML
PhyML/FastTree
i-ADHoRe

But the good news is that most of the software it depends on can be installed with bioconda

conda create -n wgd python=3.5 blast mcl muscle mafft prank paml fasttree cmake libpng mpi=1.0=mpich
conda activate wgd

Here mpi=1.0=mpich is selected, because i-adhore depends on mpich. If openmpi is installed, an error will appear while loading shared libraries: libmpi_cxx.so.40: cannot open shared object file: No such file or directory

After that, the installation is much simpler

git clone https://github.com/arzwa/wgd.git
cd wgd
pip install .
pip install git+https://github.com/arzwa/wgd.git
For i-ADHoRe, you need to register at http:// bioinformatics.psb.ugent.be /webtools/i-adhore/licensing/Agree to the license to download i-ADHoRe-3.0

Since my miniconda3 installed ~/opt/, the installation path is so~/opt/miniconda3/envs/wgd/

tar -zxvf i-adhore-3.0.01.tar.gz
cd i-adhore-3.0.01
mkdir -p build && cd build
cmake .. -DCMAKE_INSTALL_PREFIX=~/opt/miniconda3/envs/wgd/
make -j 4
make insatall

Take the sugarcane genome Saccharum spontaneum L as an example. The genome is 8-ploid with 32 chromosomes (2n = 4x8 = 32)

Download the tutorial for CDS and GFF annotation files

mkdir -p wgd_tutorial && cd wgd_tutorial
wget http://www.life.illinois.edu/ming/downloads/Spontaneum_genome/Sspon.v20190103.cds.fasta.gz
wget http://www.life.illinois.edu/ming/downloads/Spontaneum_genome/Sspon.v20190103.gff3.gz
gunzip *.gz

First conda activate wgdstart our analysis environment, and then start the analysis

Step 1 : Use to wgd mclidentify homologous genes in the genome

wgd mcl -n 20 --cds --mcl -s Sspon.v20190103.cds.fasta -o Sspon_cds.out

Step 2 : Use to wgd ksdbuild Ks distribution

wgd ksd --n_threads 80 Sspon_cds.out/Sspon.v20190103.cds.fasta.blast.tsv.mcl Sspon.v20190103.cds.fasta

Step 3 : If the quality of the genome is good, then wgd syncollinearity analysis can be used . It can help us find the collinearity block in the genome and the corresponding anchor point

wgd syn --feature gene --gene_attribute ID \
-ks wgd_ksd/Sspon.v20190103.cds.fasta.ks.tsv \
Sspon.v20190103.gff3 Sspon_cds.out/Sspon.v20190103.cds.fasta.blast.tsv.mcl

 For more reading - There are 9 sub-modules in WGD

• kde: KDE fitting to the Ks distribution
• ksd: Ks distribution construction
• mcl: BLASP comparison of All-vs-ALl + MCL classification analysis.
• mix: Hybrid modeling of Ks distribution.
• pre: preprocess the CDS file
• syn: Call I-ADHoRe 3.0 to use GFF files for collinearity analysis
• viz: draw histogram and density plot
• wf1: Ks standard analysis procedure of the whole genome paranome (paranome), call mcl, ksd and syn
• wf2: Ks standard analysis procedure of one-vs-one homologous gene (ortholog), call wcl and kSD

This course is organized with support from the IAP “Belgian Medical Genomics Initiative”, SymBioSys and the Genomics Core.

For inquiries, please email Ms Narcisse Opdekamp ( narcisse.opdekamp@uzleuven.be ).

More at >> http://gc.uzleuven.be/

WALK-IN-INTERVIEW

A walk-in-Interview is proposed to be held at National Bureau of Animal Genetic Resources, Karnal (Haryana)-132001 at 11:30 AM on 18.12.2013 to select One RA and One SRF as per details given below:

1. One post of Research Associate under DBT sponsored Support under BIPP for the “SanGenix: A comprehensive Next Generation Sequence (NGS) data analysis solution” as Grants in AID. Thepost duration is Upto 31st March 2015 or earlier.

2. One post of Senior Research Fellow under NAIP (Component-4) Bioprospecting of genes and allele mining for abiotic stress tolerance. The post duration is Upto 31st March 2014 or earlier

Essential Qualifications: Ph.D. in Bioinformatics/ Computer Application or
First Class Masters degree in Bioinformatics/ Computer Application with two years experience as evidenced by Publications.

Desirable: Experience in the field of handling Next generation Sequencing Data.

Emolument: Rs. 22,000/- per month + HRA as per admissibility

Age Limit:

40 years for Men
45 years for women as on date of interview

Research Associate: ONE

Duration of engagement: Upto

31st March 2015 or earlier & Coterminus with the project

Responsibilities: To help the PI for Beta testing and development of the SanGenix Tool for NGS data.

Essential Qualifications: First Class Masters’ degree in Bioinformatics/Biotechnology.

Desirable: Experience in the field of Biotechnology/ Bioinformatics

Emoluments:

Rs. 16,000/- per month + HRA as per admissibility.
Senior Research Fellow: ONE
Duration of engagement: Upto 31st March 2014 or earlier & Coterminus with the project

Age Limit

35 years for men
40 years for women as on date of interview

Note: Relaxation in age will be admissible for SC/ST & OBC candidates as per Govt. of India /ICAR norms

1. The applicants must bring with them original documents and brief of research work done during post graduation along with a set of photocopy and latest two passport size photographs.
2. A panel of selected candidates will also be made which may be utilized for filling of positions of shorter durations in future if demand arises.
3. Experience certificate in original, if any 4. The above positions are purely on temporary basis and are co-terminus with the project. No TA/DA will be paid to attend the interview.
5. Any other clarifications can be had on the date of interview.
6. The Director’s decision will be final and binding on all respects.

Advertisement: http://210.212.93.85/rasrfadvertise.pdf

Perl one-liners are small and awesome Perl programs that fit in a single line of code and they do one thing really well. These things include changing line spacing, numbering lines, doing calculations, converting and substituting text, deleting and printing certain lines, parsing logs, editing files in-place, doing statistics, carrying out system administration tasks, updating a bunch of files at once, and many more. Perl one-liners will make you the shell warrior. Anything that took you minutes to solve, will now take you seconds!

perl -pe '$\="\n"'   
#double space a file

perl -pe '$_ .= "\n" unless /^$/'
#double space a file except blank lines

perl -pe '$_.="\n"x7'
#7 space in a line.

perl -ne 'print unless /^$/'
#remove all blank lines

perl -lne 'print if length($_) < 20'
#print all lines with length less than 20.

perl -00 -pe ''
#If there are multiple spaces, delete all leaving one(make the file a single spaced file).

perl -00 -pe '$_.="\n"x4'
#Expand single blank lines into 4 consecutive blank lines

perl -pe '$_ = "$. $_"'
#Number all lines in a file

perl -pe '$_ = ++$a." $_" if /./'
#Number only non-empty lines in a file

perl -ne 'print ++$a." $_" if /./'
#Number and print only non-empty lines in a file

perl -pe '$_ = ++$a." $_" if /regex/'
#Number only lines that match a pattern

perl -ne 'print ++$a." $_" if /regex/'
#Number and print only lines that match a pattern

perl -ne 'printf "%-5d %s", $., $_ if /regex/'
#Left align lines with 5 white spaces if matches a pattern (perl -ne 'printf "%-5d %s", $., $_' : for all the lines)

perl -le 'print scalar(grep{/./}<>)'
#prints the total number of non-empty lines in a file

perl -lne '$a++ if /regex/; END {print $a+0}'
#print the total number of lines that matches the pattern

perl -alne 'print scalar @F'
#print the total number fields(words) in each line.

perl -alne '$t += @F; END { print $t}'
#Find total number of words in the file

perl -alne 'map { /regex/ && $t++ } @F; END { print $t }'
#find total number of fields that match the pattern

perl -lne '/regex/ && $t++; END { print $t }'
#Find total number of lines that match a pattern

perl -le '$n = 20; $m = 35; ($m,$n) = ($n,$m%$n) while $n; print $m'
#will calculate the GCD of two numbers.

perl -le '$a = $n = 20; $b = $m = 35; ($m,$n) = ($n,$m%$n) while $n; print $a*$b/$m'
#will calculate lcd of 20 and 35.

perl -le '$n=10; $min=5; $max=15; $, = " "; print map { int(rand($max-$min))+$min } 1..$n'
#Generates 10 random numbers between 5 and 15.

perl -le 'print map { ("a".."z",”0”..”9”)[rand 36] } 1..8'
#Generates a 8 character password from a to z and number 0 – 9.

perl -le 'print map { ("a",”t”,”g”,”c”)[rand 4] } 1..20'
#Generates a 20 nucleotide long random residue.

perl -le 'print "a"x50'
#generate a string of ‘x’ 50 character long

perl -le 'print join ", ", map { ord } split //, "hello world"'
#Will print the ascii value of the string hello world.

perl -le '@ascii = (99, 111, 100, 105, 110, 103); print pack("C*", @ascii)'
#converts ascii values into character strings.

perl -le '@odd = grep {$_ % 2 == 1} 1..100; print "@odd"'
#Generates an array of odd numbers.

perl -le '@even = grep {$_ % 2 == 0} 1..100; print "@even"'
#Generate an array of even numbers

perl -lpe 'y/A-Za-z/N-ZA-Mn-za-m/' file
#Convert the entire file into 13 characters offset(ROT13)

perl -nle 'print uc'
#Convert all text to uppercase:

perl -nle 'print lc'
#Convert text to lowercase:

perl -nle 'print ucfirst lc'
#Convert only first letter of first word to uppercas

perl -ple 'y/A-Za-z/a-zA-Z/'
#Convert upper case to lower case and vice versa

perl -ple 's/(\w+)/\u$1/g'
#Camel Casing

perl -pe 's|\n|\r\n|'
#Convert unix new lines into DOS new lines:

perl -pe 's|\r\n|\n|'
#Convert DOS newlines into unix new line

perl -pe 's|\n|\r|'
#Convert unix newlines into MAC newlines:

perl -pe '/regexp/ && s/foo/bar/'
#Substitute a foo with a bar in a line with a regexp.

Reference/Sources:

http://genomics-array.blogspot.in/2010/11/some-unixperl-oneliners-for.html

http://genomespot.blogspot.com/2013/08/a-selection-of-useful-bash-one-liners.html

http://biowize.wordpress.com/2012/06/15/command-line-magic-for-your-gene-annotations/

http://genomics-array.blogspot.com/2010/11/some-unixperl-oneliners-for.html

http://bioexpressblog.wordpress.com/2013/04/05/split-multi-fasta-sequence-file/

De Bruijn Graphs for NGS Assembly
Algorithms for PacBio Reads
Software and Hardware Concepts for Bioinformatics
Finding us in Homolog.us (Search Algorithms)
NGS Genome and RNAseq Assembly - a Hands on Primer
Introduction to PERL, Python, R and C/C++ for Bioinformatics

Address of the bookmark: http://www.homolog.us/Tutorials/

Our main advantages over other similar tools are:

• GeneAnalytics is very simple and intuitive to use.
• GeneAnalytics is based on our proprietary databases – GeneCards, MalaCards, PathCards and LifeMap Discovery, each of them integrates information from a very large number of resources.
• GeneAnalytics supplies links for extensive background information on each of the matched results.

I invite you to try it out for free at geneanalytics.genecards.org, and would be happy to hear your comments and thoughts on how we can improve.

Yours,

Shani Ben-Ari Fuchs

LifeMap Sciences Team

http://rosalind.info/problems/list-view/

Address of the bookmark: http://rosalind.info/problems/list-view/

NAME OF THE POST : Bioinformatician (Part time 3 days in a week) (One Position only)

DURATION : One Year

NAME OF THE PROJECT : Next generation sequencing facility

EDUCATIONAL QUALIFICATIONS : At least a Masters degree in Bioinformatics and Bachelors degree in any stream of life sciences

REQUIREMENTS :

Around 5 years of experience and proven track record in next generation sequence data analysis (supported by publications in peer-reviewed journals), ability to analyze transcriptomics, Chip-seq, and small RNA –seq data.

: Should have the ability to analyze raw primary data generated by Illumina next generation sequencing platforms and create / troubleshoot custom analysis Pipelines.

Should have ability to handle all downstream secondary and tertiary data analysis using commercially available as well as open source softwares (transcriptomics, ChIP-seq, small RNA-seq)

Apart from these, the applicant should have knowledge of the following: Programming: Perl and Python. Operating system:

Linux and Windows. NGS Analysis tools: Maq, BWA, Bowtie, SAM tools, BEDTools, MACS, Galaxy, FastQC, Bismark, MEDIPS, Tophat, Cufflinks, AvadisNGS, CLC Genomics Workbench, Galaxy, BaseSpace, Trinity Statistics: Microsoft Excel and R. Database: MySQL Genome Browser: UCSC, Ensemble, IGV, IGB Motif Analysis Tools: MEME Suite, Transfac and RSAT Functional Annotation Tools: DAVID, GeneCodis, Gene Cards Networking Tools: Cytoscape

EMOLUMENTS : The incumbent will be paid a fee of Rs. 2000/- per sitting/ per day.

SCIENTIST NAME : Dr. Arnab Mukhopadhyay,

Staff Scientific V Next generation sequencing facility

SCIENTIST’S E-MAIL ID : arnab@nii.ac.in

WALK IN INTERVIEW ON : 18th September, 2015

REGISTRATION OF CANDIDATES: 10.30 AM to 11.00 AM

PLEASE NOTE- 1. CANDIDATE MAY FILL UP APPLICATION IN THE PRECRIBED FORMAT ALONG WITH NECESSARY DOCUMENTS FOR VERIFICATION. 2. APPLICATIONS CONTAINING INCOMPLETE INFORMATION SHALL NOT BE ENTERTAINED. 3. DATE OF PASSING THE EXAMINATIONS MUST BE INDICATED CLEARLY. 4. ONLY REGISTERED CANDIDATES WILL BE INTERVIEWED. 5. NO TA/DA WILL BE PAID FOR ATTENDING THE INTERVIEW PRESCRIBED FORM 1. NAME 2. FATHER’S NAME 3. MOTHER’S NAME 4. DATE OF BIRTH 5. SEX (MALE/FEMALE) 6. CATEGORY (SC/ ST/ OBC/ PH) 7. ADDRESS a. (CORRSPONDENCE) b. (PERMANENT) 8. E MAIL, TELEPHONE NO. & MOBILE No (if any) 9. ACADEMIC & PROFESSIONAL QUALIFICATIONS NAME OF EXAMINATION PASSED WITH SUBJECTS YEAR OF PASSING BOARD/ UNIVERSITY PERCENTAGE/ DIVISION REMARKS 10. PAST EXPERIENCE & PRESENT EMPLOYMENT, IF ANY 11. CANDIDATES SHOULD STATE CLEARLY WHETHER THEY HAVE BEEN AWARDED PH.D DEGREE OR THESIS HAS BEEN SUBMITTED. 12. HAVE YOU APPLIED FOR A POSITION EARLIER IN THE INSTITUTE? IF SO:- (1) THE DETAILS OF THE PROJECT AND PROJECT INVESTIGATOR (2) IF CALLED FOR INVERVIEW, RESULTS THEREOF

More at http://www1.nii.res.in/sites/default/files/walkininterview-18sept2015.pdf

http://katjulab.com/research.html