The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed... go to blog

The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed... go to blog

As most textbooks would have it, the term “junk DNA” was coined in 1972 by Susumu Ohno as part of his work on the role of gene and genome duplication. The first time I met Susumu Ohno was at a meeting in Crete many years ago, and the way I remember it, he told me that he “deliberately” chose a “provocative term” for “junk DNA” to emphasize the “uselessness” of this DNA fraction. (Indeed, the term “junk” comes with a … go to blog

Careers in training! go to blog

The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed... go to blog

The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed... go to blog

PacBio has made its reputation delivering very high accuracy long reads, which they have branded HiFi. These are based on their circular consensus technology: each template DNA molecule is converted into a single continuous circle of DNA which can be read in a rolling circle reaction. The "movie" is converted to raw base calls and the adapters are clipped out, leaving "subreads" which can be aligned together to generate a consensus (CCS) read. With many passes over the same molecule … go to blog

The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed... go to blog

The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed... go to blog

Definition. The dual assembly of a diploid sample consists of two sets of contigs with each set representing one complete haploid genome. Similar to contigs in a primary assembly, contigs in a dual assembly may have occasional switches between parental haplotypes. I called such an assembly as partially phased assembly in an earlier post but decided to coin a new term in our new hifiasm preprint for clarity. Why dual assembly? A primary or collapsed assembly only represents one haploid … go to blog

The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed... go to blog

Was recently asked about HGVS nomenclature reporting. The fun thing about biology is that there's going to be exceptions to the rule or some shenanigans that you didn't expect when setting out a rule. "The Human Genome Variation Society (HGVS) provides standardized recommendations for describing human sequence variants, which are widely accepted in the scientific community, especially in the practice of clinical molecular pathology.1 Use of the HGVS nomenclature system is a de facto recommendation for clinical reporting of sequence … go to blog

Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers | Nature Methods https://www.nature.com/articles/s41592-021-01254-9Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers | Nature MethodsThe rapid growth of high-throughput technologies has transformed biomedical research. With the increasing amount and complexity of data, scalability and reproducibility have become essential not ...www.nature.comhttps://github.com/GoekeLab/bioinformatics-workflows GitHub - GoekeLab/bioinformatics-workflows: minimal example implementations for bioinformatics workflow managersWorkflow managers provide an easy and intuitive way to simplify pipeline development. Here we provide basic proof-of-concept implementations for selected … go to blog

strand bias and orientation bias – GATK (broadinstitute.org)"The read orientation artifact, also known as the orientation bias artifact, arises due to a chemical change in the nucleotide during library prep that results in, for example, G base-paring with A. This kind of artifact has a clear signature (e.g. C to A SNP that occurs predominantly for the middle C in the DNA sequence CCG), and it’s singlestranded in nature. Downstream, this artifact manifests as low allele fraction SNPs whose evidence … go to blog

The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed... go to blog

Just realised that other than vcf-compare and bedtools intersect there's other options https://github.com/RealTimeGenomics/rtg-toolshttps://github.com/Illumina/hap.py Also there's actually new variant callers .. Molina-Mora, J.A., Solano-Vargas, M. Set-theory based benchmarking of three different variant callers for targeted sequencing. BMC Bioinformatics 22, 20 (2021). https://doi.org/10.1186/s12859-020-03926-3 Krishnan, V., Utiramerur, S., Ng, Z. et al. Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays. BMC Bioinformatics 22, 85 (2021). https://doi.org/10.1186/s12859-020-03934-3Additional file 23: File 3. verify_variants.py Zook, Justin M et … go to blog

The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed... go to blog

If you have had to upload omics data to GEO before, you'll know it's a bit of a hassle and takes a long time. There are a few methods suggested by the GEO team if you are using the Unix command line: Using 'ncftp'ncftpset passive onset so-bufsize 33554432open ftp://geoftp:yourpasscode@ftp-private.ncbi.nlm.nih.govcd uploads/your@mail.com_yourfolderput -R Folder_with_submission_filesUsing 'lftp'lftp ftp://geoftp:yourpasscode@ftp-private.ncbi.nlm.nih.govcd uploads/your@mail.com_yourfoldermirror -R Folder_with_submission_filesUsing 'sftp' (expect slower transfer speeds since this method encrypts on-the-fly)sftp geoftp@sftp-private.ncbi.nlm.nih.govpassword: yourpasscodecd uploads/your@mail.com_yourfoldermkdir new_geo_submissioncd new_geo_submissionput file_nameUsing 'ncftpput' (transfers from the command-line without entering … go to blog

So our preprint is online called “Guidelines for reliable and reproducible functional enrichment analysis” so I thought I’d give you an overview.Enrichment analysis is widely used for exploration and interpretation of omics data, but I’ve noticed sloppy work is becoming more common. Over the past few years I’ve been asked to review several manuscripts where the enrichment analysis was poorly conducted and reported. Examples of this include lack of FDR control, incorrect background gene list specification and lack of essential … go to blog

The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed... go to blog

snakemake is awesome go to blog

The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed... go to blog

The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed... go to blog

(a) 1616: A movement or change of position, e.g., “The nature of this Euolution is clearely to leaue the File-leaders in front, and Bringers in reare.”(b) 1624: The process of unrolling, opening out, or revealing.© 1671: The process by which living organisms or their parts develop from a rudimentary to a mature or complete state. These days, this process is referred to as “development.” The first use of “evolution” in this sense appears in an anonymous book review published in … go to blog

A letter from the President of University of Houston, Renu Khator, landed in my inbox on August 10 at 1:00 PM. I was waiting for such a letter to see how a responsible university president will deal with the inane rules of Texas governor, Greg Abbott, who decreed that public schools are require marks, proof of vaccination, testing, or social distancing. I was also looking—most probably naively—at some signs of civic responsibility, of putting the interests of her “subjects” above … go to blog

The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed... go to blog

I was on vacation early this week when the news broke that PacBio has acquired HMW DNA solid phase extraction kit maker Circulomics -- the kind of vacation that I need where the scenery is gorgeous and the internet access terrible. Where solid phase means monumental slabs of granite with diabase intrusions being attacked by a high salt liquid phase. Where I actually sighted Atlantic Puffins and didn't once think about sequencing their genomes ('til now!). But now I'm back … go to blog

The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed... go to blog

It’s an old favourite of this blog, isn’t it. We had Gene name errors and Excel: lessons not learned (2012). Followed by Data corruption using Excel: 12+ years and counting (2016). Perhaps most depressingly of all, the conclusion of the trilogy, When your tools are broken, just change the data (2019-20). Well, I’m happy (?) … Continue reading Gene names, data corruption and Excel: a 2021 update go to blog

Our latest article "Gene name errors: Lessons not learned" previously @biorxiv_genomic has just been published in PLoS Computational Biology (link here). In this post I'll walk you through why it is so important to how computational biology is done. If you are a regular GenomeSpot reader you are probably well aware about how Excel mangles gene names. So why the need for a 2021 update? Well we thought that the broader genomics community would know about it by now. It … go to blog