More at http://pythonhosted.org/pybedtools/

A powerful toolset for genome arithmetic.http://code.google.com/p/bedtools/

• Binaries for Linux/macOS
• From sources for Linux/macOS
• From sources for Windows

Address of the bookmark: https://github.com/imgag/ngs-bits

https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.html

Address of the bookmark: https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.html

Essential qualifications for JRF
: M. Sc. in Bioinformatics with experience in Proteomics, genomics and structural biology. Knowledge of programming language, pearl and database – HTML, CSS,php and Java script.
Essential qualifications for Research Associate:
MSc/MTech in Bioinformatics with three years experience or Ph.D in Bioinformatics with experience in proteomics, genomics and structural biology. Knowledge of programming language, perl and database
– HTML, CSS, Java script. NGS sequence assembly and analysis and algorithm designing.
Age limit : 35 years maximum (5 year relaxation for SC/ST and women candidates)
Emoluments:
JRF: 16,000 + 30% HRA
.
Res Assoc: Rs22,000 + 30% HRA
The post is purely temporary in nature and is co-terminus with the project. The appointment would be initially for one year and may be extended further upon satisfactory performance.
Interested candidates
should send the duly filled application forms (format in the following page ) so as to reach on or before 20.9.2014 along with all the relevant documents.

More at http://www.iari.res.in/files/JRF_RA-03092014-20140903-135319.pdf

So far miniasm is in early development stage. It has only been tested on a dozen of PacBio and Oxford Nanopore (ONT) bacterial data sets. Including the mapping step, it takes about 3 minutes to assemble a bacterial genome. Under the default setting, miniasm assembles 9 out of 12 PacBio datasets and 3 out of 4 ONT datasets into a single contig. The 12 PacBio data sets are PacBio E. coli sample, ERS473430, ERS544009, ERS554120, ERS605484, ERS617393, ERS646601, ERS659581, ERS670327, ERS685285, ERS743109 and a deprecated PacBio E. coli data set. ONT data are acquired from the Loman Lab.

For a C. elegans PacBio data set (only 40X are used, not the whole dataset), miniasm finishes the assembly, including reads overlapping, in ~10 minutes with 16 CPUs. The total assembly size is 105Mb; the N50 is 1.94Mb. In comparison, the HGAP3produces a 104Mb assembly with N50 1.61Mb. This dotter plot gives a global view of the miniasm assembly (on the X axis) and the HGAP3 assembly (on Y). They are broadly comparable. Of course, the HGAP3 consensus sequences are much more accurate. In addition, on the whole data set (assembled in ~30 min), the miniasm N50 is reduced to 1.79Mb. Miniasm still needs improvements.

Miniasm confirms that at least for high-coverage bacterial genomes, it is possible to generate long contigs from raw PacBio or ONT reads without error correction. It also shows that minimap can be used as a read overlapper, even though it is probably not as sensitive as the more sophisticated overlapers such as MHAP and DALIGNER. Coupled with long-read error correctors and consensus tools, miniasm may also be useful to produce high-quality assemblies.

Minimap and miniasm are ultrafast tools for (i) mapping and (ii) assembly. Designed for long, noisy reads, they do not have a correction or consensus step, and therefore the resulting assemblies are contiguous (i.e. long) but very noisy (i.e. full of errors)

We start with an all against all comparison:

minimap -Sw5 -L100 -m0 -t8 reads.fq reads.fq | gzip -1 > reads.paf.gz

Then we can assemble

miniasm -f reads.fq reads.paf.gz > reads.gfa

Convert GFA to FASTA:

awk '/^S/{print ">"$2"\n"$3}' reads.gfa | fold > reads.fa

And then count how many contigs:

grep ">" reads.fa | wc -l

# Download sample PacBio from the PBcR website
wget -O- http://www.cbcb.umd.edu/software/PBcR/data/selfSampleData.tar.gz | tar zxf -
ln -s selfSampleData/pacbio_filtered.fastq reads.fq
# Install minimap and miniasm (requiring gcc and zlib)
git clone https://github.com/lh3/minimap && (cd minimap && make)
git clone https://github.com/lh3/miniasm && (cd miniasm && make)
# Overlap
minimap/minimap -Sw5 -L100 -m0 -t8 reads.fq reads.fq | gzip -1 > reads.paf.gz
# Layout
miniasm/miniasm -f reads.fq reads.paf.gz > reads.gfa

Address of the bookmark: https://github.com/lh3/miniasm

Find the detail of the reads repeats:

fq2fa ONT_A.fastq ONT_A.fasta 

minimap2 -xava-ont ONT_A.fasta ONT_A.fasta -t10 -X > AONT.paf 

awk '{if($1==$6){print}}' AONT.paf > AONTself.paf 

awk '$5=="-"' AONTself.paf | awk '{print $1}'| sort|uniq > invertedrepeat.list

Generated a few palindrome and repeats plots (highlighting only repeats largest than 10, 20 and 30 kb)

minidot -f 5 -m 30000 AONTself.paf > AONTself30000.eps 
sed 's/_template_pass_FAH31515//' AONTself30000.eps > AONTself30000final.eps 

minidot -f 5 -m 20000 AONTself.paf > AONTself20000.eps 
sed 's/_template_pass_FAH31515//' AONTself20000.eps > AONTself20000final.eps 

minidot -f 5 -m 10000 AONTself.paf > AONTself10000.eps 
sed 's/_template_pass_FAH31515//' AONTself10000.eps > AONTself10000final.eps 

Assemble with miniasm:

miniasm -f ONT_A.fasta AONT.paf > AONT.gfa 

grep '^S' AONT.gfa |awk '{print ">"$2"\n"$3}' > AONT_miniasm.fasta 

minimap2 -xasm10 AONT_miniasm.fasta AONT_miniasm.fasta -t1 -X > AONT_miniasm.paf 

awk '{if($1==$6){print}}' AONT_miniasm.paf > AONT_miniasm_self.paf 

minidot -f 5 -m 10000 AONT_miniasm_self.paf > AONT_miniasm_self10000.eps 

Njoy the assembly !

ADVERTISEMENT NO. - URDIP/ 5/2014

Learning opportunity for young Science and Engineering professionals to make a career in Information Science Industry CSIR has set up a Unit for Research and Development of Information Products (CSIR-URDIP) at Pune to work in the area of Scientific Informatics (ChemBioinformatics/Patent Informatics/Phytoinformatics/Toxinformatics) and related
software development projects.

Applications are invited from CSIR - UGC NET Qualified Candidates for consideration as Project Fellow (PF) and/or Senior Project Fellow (SPF) based on the experience to work on existing and new projects at CSIRURDIP.

Project Fellow

Remuneration - (Rs. 16,000.00 + 20% HRA)

M. Sc. In Biochemistry/Microbiology/Bioinformatics [Post-code A02] only with minimum of 55% marks

Senior Project Fellow

Remuneration - (Rs. 18,000.00 + 20% HRA)

M. Sc. in Biochemistry/Microbiology/Bioinformatics [Post-code A05] only with minimum of 55% marks plus two years research or relevant informatics experience

Please visit www.urdip.res.in/career.htm to apply online by 30th September, 2014.

Successful candidates who have appeared for NET exam in 2012 and 2013 are only eligible to apply.

Advertisement: http://115.112.95.114/urhr/download/Advt5_2014.pdf

Address of the bookmark: https://github.com/fenderglass/Flye

Eligible candidates are invited for a walk-in-interview for recruitment of Project Assistant in SVIMS Bioinformatics centre under the BTISnet Project entitled “Creation of Bioinformatics Infrastructure Facility for promotion of Biology teaching through Bioinformatics” on 25.09.2014 at 11 AM in SVIMS, Tirupati. The engagement will be made purely on temporary basis for a period of one year and it can be terminated at any time without notice or without assigning any reason thereof by the Coordinator of the Project. The person engaged shall not be entitled for any claim implicit or explicit for absorption in the University.

1. Name of the post : Project Assistant

2. Qualification :
i) Essential : MSc Bioinformatics/MTech (Biotechnology/Bioinformatics)

ii) Desirable : Experience in Bioinformatics research work (Preference will be given to candidates qualified in BINC/UGC/CSIR/NET/GATE)

3. Remuneration : 16000 + 10% HRA for NET/GATE candidates 14000 + 10% HRA for M. Tech / M.Sc. Candidates

4. Place of posting : Tirupati

5. Duration of the Project : One year

Terms and conditions:

1. Candidates are required to submit the Biodata relevant certificates in support of their age and educational qualification etc., before the interview committee, SVIMS University, Tirupati.

2. Candidates called for interview will attend the interview at their own cost.
3. Interim enquiries will not be entertained.
4. The maximum age limit for Project Assistant is 28 years for general category and 33 years for SC and ST category candidates as on 25th September, 2014.

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http://svr98.ehostpros.com/~svimsb98/Project%20Assistant_notification.pdf