<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/41146?offset=170 https://bioinformaticsonline.com/pages/view/40248/industrial-training-in-computer-aided-drug-designing-cadd Wed, 13 Nov 2019 05:00:44 -0600 https://bioinformaticsonline.com/pages/view/40248/industrial-training-in-computer-aided-drug-designing-cadd <![CDATA[Industrial Training in Computer Aided Drug Designing (CADD)]]> Learn More about  Computer Aided Drug Designing (CADD)!!!

#rasalsi #rasa In our Industrial program you will get Knowledge on RNA Seq, CHIP Seq,

Batch Starts From 18th November 2019

#hurryup #registernow #enquirenow The primary goal of the industrial training program is to provide students with necessary skills making with employable. RASA LSI trains students with the enhanced skills required for them to excel in jobs in biotechnology, pharmaceuticals, BioIT and related industry sectors. At Rasa you will  learn from industry leaders how to apply these skills in life science & have a command over software developing process  by using various methodologies. For Registration visit us on: https://www.rasalsi.com/index.php/front-page/industrial-training/

]]> RASA Life Sciences https://bioinformaticsonline.com/opportunity/view/41041/post-doc-computational-biology-bioinformatics-network-biology-data-science-ngs-mfd Sat, 15 Feb 2020 06:13:35 -0600 <![CDATA[Post Doc Computational Biology, Bioinformatics - Network Biology & Data Science, NGS (m/f/d)]]> https://www.jobvector.de/jobs-stellenangebote/biologie-life-sciences/forschung-entwicklung/post-doc-computational-biology-bioinformatics-network-biology-data-science-ngs-129867.html?suid=e522e9793b41817e52ac58d6963b94e2519920df

Requirements
Doctoral degree in Bioinformatics, Computational Biology, (Bio)physics/-mathematics, Biochemistry/Biology or similar with strong quantitative and numeric focus
Ability to numerically process complex and large data sets
Good programming skills (R/Bioconductor and/or Python preferred, Linux is a plus)
Experience in analyzing next-generation sequencing data sets using network biology
Scientific publication record in applied bioinformatics
Familiarity with single cell NGS analyses and other –omics techniques is a plus, but not essential

]]> https://bioinformaticsonline.com/bookmarks/view/42917/fings-filters-for-next-generation-sequencing Sat, 27 Feb 2021 01:18:35 -0600 https://bioinformaticsonline.com/bookmarks/view/42917/fings-filters-for-next-generation-sequencing <![CDATA[FiNGS: Filters for Next Generation Sequencing]]> Key features
  • Filters SNVs from any variant caller to remove false positives
  • Calculates metrics based on BAM files and provides filtering not possible with other tools
  • Fully user-configurable filtering (including which filters to use and their thresholds)
  • Option to use filters identical to ICGC recommendations

FiNGS provides researchers with a tool to reproducibly filter somatic variants that is simple to both deploy and use, with filters and thresholds that are fully configurable by the user. It ingests and emits standard variant call format (VCF) files and will slot into existing sequencing pipelines. It allows users to develop and implement their own filtering strategies and simple sharing of these with others.

FiNGS reliably improves upon the precision of default variant caller outputs and performs better than other tools designed for the same task.

Address of the bookmark: https://github.com/cpwardell/FiNGS

]]> Neel https://bioinformaticsonline.com/pages/view/37411/my-commonly-used-commands-in-bioinformatics Thu, 26 Jul 2018 04:58:45 -0500 https://bioinformaticsonline.com/pages/view/37411/my-commonly-used-commands-in-bioinformatics <![CDATA[My commonly used commands in Bioinformatics]]> FYI, I've found it useful to use MUMmer to extract the specific changes that Racon makes, so I can evaluate them individually:

minimap -t 24 assembly.fasta long_reads.fastq.gz | racon -t 24 long_reads.fastq.gz - assembly.fasta racon_assembly.fasta
nucmer -p nucmer assembly.fasta racon_assembly.fasta
show-snps -C -T -r nucmer.delta

This reports Racon's changes in a table. You can exclude indels with the -I option in show-snps. 

This process (Racon -> MUMmer -> SNP table) solves the problem I originally raised in this issue. So as far as I'm concerned, you can close this issue (or keep it open if you still want to implement some kind of variant table).

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/38199/pacasus-correction-of-palindromes-in-long-reads-from-pacbio-and-nanopore Mon, 12 Nov 2018 05:26:48 -0600 https://bioinformaticsonline.com/bookmarks/view/38199/pacasus-correction-of-palindromes-in-long-reads-from-pacbio-and-nanopore <![CDATA[Pacasus: Correction of palindromes in long reads from PacBio and Nanopore]]>
Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification. Check the poster from the Revolutionizing Next-Generation Sequencing (2nd edition) conference in the source folder: https://github.com/swarris/Pacasus/blob/master/vib2017.pdf.

The prepint version is found on http://www.biorxiv.org/content/early/2017/08/09/173872

It uses the pyPaSWAS framework for sequence alignment (https://github.com/swarris/pyPaSWAS)

Address of the bookmark: https://github.com/swarris/Pacasus

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/40544/ngs-bits-short-read-sequencing-tools Thu, 16 Jan 2020 23:14:00 -0600 https://bioinformaticsonline.com/bookmarks/view/40544/ngs-bits-short-read-sequencing-tools <![CDATA[ngs-bits - Short-read sequencing tools]]> Binaries of ngs-bits are available via Bioconda. Alternatively, ngs-bits can be built from sources:

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

]]> Neel https://bioinformaticsonline.com/bookmarks/view/40754/understanding-your-reads-and-mapping Wed, 29 Jan 2020 06:29:55 -0600 https://bioinformaticsonline.com/bookmarks/view/40754/understanding-your-reads-and-mapping <![CDATA[Understanding your reads and mapping !]]> One of the best tutorial for beginners ...

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

]]> Neel https://bioinformaticsonline.com/bookmarks/view/33660/equant-energy-based-quality-assessment-of-protein Sat, 24 Jun 2017 19:24:24 -0500 https://bioinformaticsonline.com/bookmarks/view/33660/equant-energy-based-quality-assessment-of-protein <![CDATA[eQuant : energy-based quality assessment of protein]]> Protein structures are of varying quality. Especially, in-silico modeled structures are prone to contain serious errors, which limit the usefulness and reliability of these particular protein structures.

eQuant is a service for structure quality assessment of single proteins, which utilizes a coarse-grained energy model. The overall quality is calculated as well as the reliability of individual residues. You can submit single PDB files or archives containing a set of proteins.

https://biosciences.hs-mittweida.de/equant/

Address of the bookmark: https://biosciences.hs-mittweida.de/equant/

]]> Shruti Paniwala https://bioinformaticsonline.com/bookmarks/view/41831/merqury-reference-free-quality-and-phasing-assessment-for-genome-assemblies Sat, 06 Jun 2020 05:38:34 -0500 https://bioinformaticsonline.com/bookmarks/view/41831/merqury-reference-free-quality-and-phasing-assessment-for-genome-assemblies <![CDATA[Merqury: reference-free quality and phasing assessment for genome assemblies]]> Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality reference. Merqury provides a set of tools for this purpose.

https://github.com/marbl/meryl

Address of the bookmark: https://github.com/marbl/merqury

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44476/omark-software-for-proteome-protein-coding-gene-repertoire-quality-assessment Wed, 21 Feb 2024 15:01:20 -0600 https://bioinformaticsonline.com/bookmarks/view/44476/omark-software-for-proteome-protein-coding-gene-repertoire-quality-assessment <![CDATA[OMArk: software for proteome (protein-coding gene repertoire) quality assessment]]> OMArk is a software for proteome (protein-coding gene repertoire) quality assessment. It provides measures of proteome completeness, characterizes the consistency of all protein coding genes with regard to their homologs, and identifies the presence of contamination from other species. OMArk relies on the OMA orthology database, from which it exploits orthology relationships, and on the OMAmer software for fast placement of all proteins into gene families.

Address of the bookmark: https://github.com/DessimozLab/OMArk

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