<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/41459?offset=770 https://bioinformaticsonline.com/blog/view/44758/the-ifs-and-buts-of-ngs-quality-control-and-trimming Thu, 02 Jan 2025 20:11:07 -0600 https://bioinformaticsonline.com/blog/view/44758/the-ifs-and-buts-of-ngs-quality-control-and-trimming <![CDATA[The "Ifs" and "Buts" of NGS Quality Control and Trimming]]> Next-Generation Sequencing (NGS) has revolutionized biological research, providing vast amounts of data for a wide range of applications. However, the reliability of NGS analyses heavily depends on the quality of raw sequencing data. Quality control (QC) and trimming are critical preprocessing steps that can make or break your downstream analyses. In this blog, we explore the "ifs" (why you should perform QC and trimming) and the "buts" (challenges or considerations) of this vital step in NGS workflows.

The "Ifs" of NGS QC and Trimming

  1. Ensures Data Integrity
    If you want to minimize errors in downstream analyses, QC and trimming remove low-quality reads and bases, ensuring high-confidence data. This step is essential for reliable variant calling, assembly, and other applications.

  2. Removes Contaminants
    If adapter sequences or contaminants are present in the raw reads, trimming can eliminate them. This prevents issues like misalignment or incorrect biological interpretations, ensuring cleaner data for analysis.

  3. Improves Mapping and Assembly
    If your goal is better alignment to a reference genome or improved de novo assembly, trimming low-quality bases and adapters is critical. High-quality reads map more efficiently and generate more accurate assemblies.

  4. Reduces Computational Load
    If you want to save computational resources, trimming reduces the dataset size, which speeds up processing and analysis. Clean datasets mean less computational time spent on processing low-quality data.

  5. Prepares for Standardized Analyses
    If your project involves multiple datasets, QC and trimming ensure uniformity across them. This standardization makes comparisons valid and reproducible, particularly in large collaborative studies.

The "Buts" of NGS QC and Trimming

  1. Risk of Over-Trimming
    But excessive trimming can lead to the loss of informative sequences, reducing read depth and potentially discarding biologically relevant data. This is especially critical in studies with limited sequencing depth.

  2. Bias Introduction
    But trimming algorithms might introduce biases, especially if they inadvertently remove sequences with specific biological patterns. This can skew results and compromise biological insights.

  3. Loss of Context in Paired-End Reads
    But trimming one read in a pair more than the other can lead to loss of pairing information. This complicates downstream analyses that rely on paired-end data, such as structural variant detection.

  4. Time and Resource Intensive
    But running QC and trimming for large datasets can be computationally expensive and time-consuming. As sequencing depth increases, preprocessing becomes a bottleneck in the analysis pipeline.

  5. Variable Standards
    But the criteria for trimming (e.g., quality threshold, minimum read length) can vary between tools and datasets. This variability may affect reproducibility and comparability of results across studies.

Balancing the "Ifs" and "Buts"

To maximize the benefits of QC and trimming while mitigating the challenges, consider the following best practices:

  • Use QC Tools Wisely: Start with tools like FastQC to identify quality issues in your raw data. Visualizing quality metrics helps tailor your trimming parameters.

  • Choose Reliable Trimming Tools: Tools like Trimmomatic, Cutadapt, and BBduk offer adaptive and customizable trimming options. Select one that aligns with your dataset and project goals.

  • Set Reasonable Parameters: Avoid over-trimming by setting quality thresholds and minimum read lengths that balance data retention and quality improvement.

  • Test Downstream Effects: Validate the impact of QC and trimming on downstream analyses, such as alignment efficiency, variant calling accuracy, or assembly quality.

  • Document Your Workflow: Maintain detailed records of the parameters and tools used for QC and trimming. This ensures reproducibility and enables better troubleshooting.

Conclusion

NGS quality control and trimming are essential steps to ensure reliable and accurate data for analysis. While the "ifs" highlight the clear benefits of these steps, the "buts" remind us of the potential pitfalls. By adopting best practices and carefully balancing these considerations, you can optimize your preprocessing workflow and unlock the full potential of your sequencing data.

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/3885/precision-medicine Sat, 24 Aug 2013 15:47:03 -0500 https://bioinformaticsonline.com/bookmarks/view/3885/precision-medicine <![CDATA[Precision Medicine]]> Coupling established clinical–pathological indexes with state-of-the-art molecular profiling to create diagnostic, prognostic, and therapeutic strategies precisely tailored to each patient's requirements — hence the term “Precision medicine” 

Source:http://www.nejm.org/doi/full/10.1056/NEJMp1114866

Another video on precision medicine:

http://www.youtube.com/watch?v=Pi8W0yOXnzE

Precision Medicine basically intergrates bioinformatics, genomics , genetics, molecular biology and nanotechnology to deliver precise cure/diagnotics to a specific patient.

Examples:

  • The drug imatinib (Gleevec) designed to inhibit an altered enzyme produced by a fused version of two genes found in chronic myelogenous leukemia.
  • The breast cancer drug trastuzumab (Herceptin) works only for women whose tumors have a particular genetic profile called HER-2 positive.

E.g. source :

http://www.bionews-tx.com/news/2013/08/15/how-the-impact-of-cancer-genomics-on-precision-medicine-is-revolutionizing-cancer-treatment/

Address of the bookmark: http://www.cbsnews.com/video/watch/?id=50149783n

]]> Rahul Agarwal https://bioinformaticsonline.com/bookmarks/view/3031/following-the-scientific-literature-a-personal-practical-guide-for-young-computational-biologists Fri, 23 Aug 2013 07:18:51 -0500 https://bioinformaticsonline.com/bookmarks/view/3031/following-the-scientific-literature-a-personal-practical-guide-for-young-computational-biologists <![CDATA[Following the scientific literature: A personal practical guide for young computational biologists]]> The goal of this guide is to describe why, when, where and how can you follow the most up-to-date science of interest and what papers/journals you should follow. The guide is biased towards the fields of genomics/systems biology.(from article)

Source:  Igor Ulitsky & Ron Shamir

Address of the bookmark: http://acgt.cs.tau.ac.il/guides/LiteratureGuide.htm

]]> Rahul Agarwal https://bioinformaticsonline.com/bookmarks/view/5402/key-bioinformatics-scientists Wed, 09 Oct 2013 13:37:07 -0500 https://bioinformaticsonline.com/bookmarks/view/5402/key-bioinformatics-scientists <![CDATA[Key Bioinformatics Scientists]]> Address of the bookmark: http://www.iscb.org/iscb-leadership-a-staff-/officers-and-board-directors

]]> Rahul Agarwal https://bioinformaticsonline.com/bookmarks/view/9586/list-of-bioinformatics-companies-and-genomics-service-providers Wed, 02 Apr 2014 06:52:28 -0500 https://bioinformaticsonline.com/bookmarks/view/9586/list-of-bioinformatics-companies-and-genomics-service-providers <![CDATA[List of bioinformatics companies and genomics service providers]]> Plz check out link for bioinformatics and genomics companies. 

Address of the bookmark: http://grouthbio.com/Genome_Software_Service.php

]]> Rahul Agarwal https://bioinformaticsonline.com/opportunity/view/17966/internship-program-for-bioinformatics-biotechnology-professionals-no-of-vacancy-2 Wed, 08 Oct 2014 01:10:08 -0500 <![CDATA[Internship Program for Bioinformatics / Biotechnology Professionals (No. Of Vacancy: 2)]]> ArrayGen is offering an Internship Program for Post graduate Bioinformatics / Biotechnology students and professionals. ArrayGen Technologies provide an excellent opportunity to gain research experience and explore if a scientific career is right for you. Currently we offer positions to outstanding students interested in Next Generation Sequencing (NGS) data analysis. Applications are accepted throughout the year. Accepted students will be listed on web with their schedules. Accepted students can attend our future workshops and trainings freely at the specified venue.

]]> https://bioinformaticsonline.com/blog/view/34912/list-of-cancer-genomics-research-web-resources Wed, 27 Dec 2017 20:33:09 -0600 https://bioinformaticsonline.com/blog/view/34912/list-of-cancer-genomics-research-web-resources <![CDATA[List of cancer genomics research web resources !]]> Major web resources for cancer genomics research

CGHub
https://cghub.ucsc.edu/
Comprehensive data repository; huge data size

EGA
https://www.ebi.ac.uk/ega/
Comprehensive data repository; huge data size

COSMIC
http://cancer.sanger.ac.uk
Largest somatic mutation database; genome sequencing paper curation

CPRG
http://www.broadinstitute.org/software/cprg
Interface for cancer program resources

GDAC
http://gdac.broadinstitute.org/
Data analysis; automatic pipelines; user-friendly reports

SNP500Cancer
http://snp500cancer.nci.nih.gov
Sequence and genotype verification of SNPs

canEvolve
www.canevolve.org/
Comprehensive analysis of tumor profile; Data from 90 studies involving more than 10,000 patients

MethyCancer
http://methycancer.psych.ac.cn
Relationship among DNA methylation, gene expression and cancer

SomamiR
http://compbio.uthsc.edu/SomamiR/
Correlation between somatic mutation and microRNA; genome-wide displaying

cBioPortal
http://www.cbioportal.org/public-portal/
Graphical summaries; gene alteration; processed data; visualization

UCSC Cancer Genomics Browser
https://genome-cancer.soe.ucsc.edu/
Clinical information; gene expression; copy number variation; visualization

CGWB
https://cgwb.nci.nih.gov/
Visualization; gene mutation and variation; automated analysis pipeline

GDSC
http://www.cancerrxgene.org
Drug sensitivity information; drug response information

canSAR
https://cansar.icr.ac.uk/
Multidisciplinary information; drug discovery

NONCODE
http://www.noncode.org/ ncRNAs;
lncRNAs; up-to-date and comprehensive resource

]]> biogeek https://bioinformaticsonline.com/news/view/38649/ngs-platforms-launched-by-bgi%E2%80%99s-mgi-tech Thu, 10 Jan 2019 04:42:06 -0600 https://bioinformaticsonline.com/news/view/38649/ngs-platforms-launched-by-bgi%E2%80%99s-mgi-tech <![CDATA[NGS Platforms launched by BGI’s MGI Tech]]> MGI Tech Co., Ltd. (MGI), a subsidiary of BGI Group, is committed to enabling effective and affordable healthcare solutions for all. Based on its proprietary technology, MGI produces sequencing devices, equipment, consumables and reagents to support life science research, medicine and healthcare. MGI's multi-omics platforms include genetic sequencing, mass spectrometry and medical imaging. Providing real-time, comprehensive, life-long solutions, its mission is to develop and promote advanced life science tools for future healthcare.

MGI, a subsidiary of global genomics leader BGI Group, announced pricing and its first early access customer for the new ultra high-throughput sequencer, MGISEQ-T7, saying it has driven down sequencing cost to $5 per gigabyte, with exceptionally high accuracy. Such innovations are helping more people to realize the benefits of genomic information.

In October, MGI launched the MGISEQ-T7, a highly flexible production-scale platform that is the most powerful sequencer to date. It can produce as many as 60 whole human genomes in one day. The instrument sells for $1 million.

The T7 enables simultaneous but independent operation of up to four flow cells, which means different applications such as single-cell RNA sequencing, whole exome sequencing and whole genome sequencing can be run in different flow cells at the same time. This helps to reduce costs, allowing MGI to offer the most competitive sequencing price in the market.

Powered by DNBseq™, MGISEQ delivers quality data with accuracy for SNP and Indel calling rate of 99.9% and 99%, respectively, along with decreased duplication rate down to less than 2 percent, and almost zero Index mis-assignment rate.

SOURCE MGI

https://www.bgi.com/global/company/news/bgis-mgi-tech-launches-two-new-ngs-platforms/

http://en.mgitech.cn/

]]> Jit https://bioinformaticsonline.com/opportunity/view/41394/ngsymposium-in-computational-biology Mon, 09 Mar 2020 06:00:30 -0500 <![CDATA[NGSymposium in Computational Biology]]> We have a great pleasure to invite you to the NGSymposium in Computational Biology to celebrate the 5th anniversary of the NGSchool Summer Schools. This international conference will make way for exchanging knowledge and experiences between experienced and early-stage researchers as well as bioinformaticians. The meeting will be held on 31.07 - 1.08.2020 in Warsaw. It will be a satellite event to the #NGSchool2020: Statistical Learning in Genomics. It will cover a wide range of topics from basic and applied biomedical sciences: bioinformatics, genomics, transcriptomics, computational biology, Machine Learning.

Registration of active participants will be open from February, 27 12 PM CET to April 17, 23:59 CET. In registration forms you will be asked for providing us with some basic information about yourself. You will also be able to submit your abstract. You can save your registration form after filling it partially and come back later to supply more data e.g. upload an abstract. Your registration will be completed only with the payment of the registration fee reaching our accounts - please make sure to transfer the money in advance!

Registration of passive participants will be open after closing of registration of active participants.

Details an registration: https://ngschool.eu/conference/

]]> https://bioinformaticsonline.com/pages/view/33837/awesome-perl-frameworks-libraries-and-software-part-1 Fri, 07 Jul 2017 04:06:59 -0500 https://bioinformaticsonline.com/pages/view/33837/awesome-perl-frameworks-libraries-and-software-part-1 <![CDATA[Awesome perl frameworks, libraries and software - PART 1]]> A curated list of awesome Perl frameworks, libraries and software.

]]> Neel