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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...

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...

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...

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...

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.

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

caffMatch is a novel scaffolding tool based on Maximum-Weight Matching able to produce high-quality scaffolds from NGS data (reads and contigs). The tool is written in Python 2.7. It also includes a bash script wrapper that calls aligner in case one...

Pharmacoinformatics jobs in Bihar http://www.rmrims.org.in/PDFs/Advertisement%20-%20Non%20Teaching%200701202016.pdf #Bihar #Pharma #Pharmainformatics #Job #RMRIMS

Learning greedy algo for biologist.  https://www.topcoder.com/community/data-science/data-science-tutorials/greedy-is-good/ This webpage is also useful for the...

Assembly and repeats https://www.coursera.org/learn/dna-sequencing/lecture/fKX4C/lecture-third-law-of-assembly-repeats-are-bad #Assembly #Repeats #Bad

It does not work if you don't have set the read-group information correctly (as is said in the breakdancer documentation). But more importantly, if you filter your results for SVs were this 11th column says that the SV is only supported by reads of...

PhD thesis and useful material on Structure Variation http://paduaresearch.cab.unipd.it/4930/1/tesi_dottorato_versione_finale.pdf

Hydra-SV The pipeline described below is meant to convey a general approach that they have found to be effective for discovering SV breakpoints with Hydra. However, it should be noted that this approach seeks to discover breakpoints arising...

This paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4479793/ provide many others tools and their comparative importance. 

I like this tool GRIDSS: the genomic rearrangement identification software suite. A high-speed next-gen sequencing structural variation caller. GRIDSS calls variants based on alignment-guided positional de Bruijn graph break-end assembly,...

The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process. EAGER encompasses both state-of-the-art tools for each step as well as new complementary tools tailored for ancient DNA data within a single...

Using breakdancer the output consists of DEL, INV, INS, CTX and ITX. Using following commands: bam2cfg.pl -g -h dis.bam normal.bam > config_file.cfgbreakdancer_max -d test config_file.cfg > dis_normal.ctx the 11th output column should...

Structural variants (SVs) such as deletions, insertions, duplications, inversions and translocations litter genomes and are often associated with gene expression changes and severe phenotypes (ie. genetic diseases in humans).

PRISM is a software for split read (reads which span across a structrual variant -- SV ) mapping and SV calling from the mapping result. PRISM is able to detect small insertions and abitrary size deletions, inversions and tandom duplications with...

Velvet advicer http://dna.med.monash.edu.au/~torsten/velvet_advisor/