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- Jit@jit.aber
Jit bookmarked PEAR 2947 days ago

PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. PEAR evaluates all possible paired-end read overlaps and without requiring the...

http://sco.h-its.org/exelixis/web/software/pear/doc.html
- Jit@jit.aber
Jit posted to the wire 2947 days ago

NGS tutorial http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/linux.html #NGS #Tutorial #Example
- Jit@jit.aber
Jit bookmarked GAM-NGS: genomic assemblies merger for next generation sequencing 2947 days ago

GAM-NGS (Genomic Assemblies Merger for Next Generation Sequencing), whose primary goal is to merge two or more assemblies in order to enhance contiguity and correctness of both. GAM-NGS does not rely on global alignment: regions of the two...

https://github.com/vice87/gam-ngs
- Jit@jit.aber
Jit bookmarked GARM:Genome Assembly, Reconciliation and Merging 2947 days ago

The pipeline is based mainly implemented using Perl scripts and modules and third-party open source software like the AMOS (Myers et al., 2000) and MUMmer (Kurtz et al., 2004) packages. The pipeline was tested on Debian, Ubuntu, Fedora and BioLinux...

http://garm-meta-assem.sourceforge.net/
- Jit@jit.aber
Jit bookmarked e-RGA: enhanced Reference Guided Assembly of Complex Genomes 2947 days ago

Next Generation Sequencing has totally changed genomics: we are able to produce huge amounts of data at an incredibly low cost compared to Sanger sequencing. Despite this, some old problems have become even more difficult, de novo assembly being on...

http://journal.embnet.org/index.php/embnetjournal/article/view/208
- Bulbul@bulbul
Bulbul posted to the wire 2947 days ago

RA Bioinformatics at NBAIR http://www.nbair.res.in/employment/RA&YP.pdf #Bioinformatics #RA #Jobs #NBAIR
- Bulbul@bulbul
Bulbul posted a new ad in the Opportunity Faculty at Indian Institute of Science Education and Research Berhampur 2947 days ago
- Jit@jit.aber
Jit bookmarked Gene Synteny Database 2950 days ago

Comparative genomics remains a pivotal strategy to study the evolution of gene organization, and this primacy is reinforced by the growing number of full genome sequences available in public repositories. Despite this growth, bioinformatic tools...

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2853686/
- Jit@jit.aber
Jit commented on the blog Tools to detect synteny blocks regions among multiple genomes 2950 days ago

R package to Finds Synteny in a Sequence Database http://origin.rdrr.io/bioc/DECIPHER/man/FindSynteny.html
- Jit@jit.aber
Jit posted to the wire 2950 days ago

Synteny database https://ecrbase.dcode.org/synteny.php #Synteny #Database
- Jit@jit.aber
Jit posted to the wire 2950 days ago

General concepts: concurrency, #parallelism, #threads and #processes http://learn-gevent-socketio.readthedocs.io/en/latest/general_concepts.html
- Jit@jit.aber
Jit posted to the wire 2950 days ago

Accept file from STDIN in Perl my $infh = \*STDIN; my $outfh = \*STDOUT #Perl #Tricks
- Jit@jit.aber
Jit commented on a bookmark QUAST: quality assessment tool for genome assemblies 2951 days ago

You can also try LAZER, it produces the same evaluation as Quast but is 5.6 times faster and use half the memory http://www.csd.uwo.ca/~ilie/LASER/
- Jit@jit.aber
Jit bookmarked E-MEM: Efficient computation of Maximal Exact Matches 2951 days ago

E-MEM is a C++/OpenMP program designed to efficiently compute MEMs between large genomes. See the README file for instructions on how to use E-MEM. E-MEM source code The source code can be downloaded here. If you use E-MEM, please...

http://www.csd.uwo.ca/~ilie/E-MEM/
- Neel@neelam
Neel bookmarked MyPro: A seamless pipeline for automated prokaryotic genome assembly and annotation 2951 days ago

MyPro is an improved genomics software pipeline for prokaryotic genomes. MyPro is user-friendly and requires minimal programming skills. High-quality prokaryotic genome assembly and annotation can be obtained with ease. It performed better than de...

http://www.sciencedirect.com/science/article/pii/S0167701215001207
- Neel@neelam
Neel bookmarked CISA: Contig Integrator for Sequence Assembly 2951 days ago

A plethora of algorithmic assemblers have been proposed for the de novo assembly of genomes, however, no individual assembler guarantees the optimal assembly for diverse species. Optimizing various parameters in an assembler is often performed in...

http://sb.nhri.org.tw/CISA/en/CISA
- Abhimanyu Singh@abhimanyu
Abhimanyu Singh bookmarked BIMA V3: an aligner customized for mate pair library sequencing 2952 days ago

Summary: Mate pair library sequencing is an effective and economical method for detecting genomic structural variants and chromosomal abnormalities. Unfortunately, the mapping and alignment of mate pair read pairs to a reference genome is a...

http://bioinformatics.oxfordjournals.org/content/early/2014/02/12/bioinformatics.btu078.full.pdf
- Bulbul@bulbul
Bulbul bookmarked Cutadapt 2952 days ago

Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Cutadapt helps with these trimming tasks by finding the adapter or primer sequences in an...

http://cutadapt.readthedocs.io/en/stable/guide.html
- Bulbul@bulbul
Bulbul commented on a bookmark List of Bioinformatics Vacancy, Jobs, Opportunity websites 2952 days ago

Thanks for the extensive list of Bioinformatics job portals. I also love to share https://www.jobvector.com/search-jobs.html?keywords=Bioinformatics&locations=&_pn=1&sort=_score job portal for bioinformatician.
- Jit@jit.aber
Jit posted to the wire 2952 days ago

Mammalian Meiotic Recombination: A Toolbox for Genome Evolution http://www.karger.com/Article/FullText/452822 #Mammals #Genome #Breakpoints #Evolution #Recombination

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