AbstractMotivation. Single-cell sequencing data analysis requires robust quality control (QC) to mitigate technical artifacts and ensure reliable downstrea

The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny.

Pangenome collections are growing to hundreds of high-quality genomes. This necessitates scalable methods for constructing pangenome alignments that can incorporate newly-sequenced assemblies. We prev...

For many years, machine learning-based ab initio gene finding approaches have been the central components of eukaryotic genome annotation pipelines, and they remain so today. The reliance on these app...

Rich Epitope Information Comes to UniProt Mammalian immune responses are mediated by interactions between antigens and immune system compo...

WABI Conference on Algorithms in Bioinformatics

Summary: Leveraging the Python/C API, eccLib was developed as a high-performance library designed for parsing genomic files and analysing genomic contexts. To the best of the authors' knowledge, it…

An efficient CLI to extract sequences from the SRA - ArcInstitute/xsra

Telomere-to-telomere (T2T) assembly is the ultimate goal for de novo genome assembly. Existing algorithms capable of near T2T assembly all require Oxford Nanopore Technologies (ONT) ultra-long reads w...

Grep for FASTQ files. Contribute to fulcrumgenomics/fqgrep development by creating an account on GitHub.

Clinical diagnosis typically incorporates physical examination, patient history, various laboratory tests, and imaging studies but makes limited use of the human immune system’s own record of antigen ...

Rust wrapper for the next generation (still currently in C++) - COMBINE-lab/piscem

Offered by Johns Hopkins University. This course will cover bioinformatics methods for analyzing transcriptomic RNA sequencing data ... Enroll for free.

Add the module "centrifuger-quant" for abundance estimation. Fix an issue in creating gtdb's taxonomy tree. (#20 ) Fix a bug that causes hit length more than read length (query length)

Despite extensive mapping of cis-regulatory elements (cREs) across cellular contexts with chromatin accessibility assays, the sequence syntax and genetic variants that regulate transcription factor (T...

The minimizer of a word of size $k$ (a $k$-mer) is defined as its smallest substring of size $m$ (with $m\leq k$), according to some ordering on $m$-mers. minimizers have been used in bioinformatics -...

Genetic diversity within the human immunoglobulin heavy chain (IGH) locus influences the expressed antibody repertoire and susceptibility to infectious and autoimmune diseases. However, repetitive seq...

Reconstructing haplotypes is important when sequencing a mixture of similar sequences. Long-read sequencing can connect distant alleles to disentangle similar haplotypes, but handling se-quencing erro...

Table of Contents 1 Introduction 1.1 Results 2 Random minimizers 3 Algorithms 3.1 Problem statement Problem A: Only the set of minimizers Problem B: The minimizer of each window Problem C: Super-k-mer...

Biocomputational method; Classification of bioinformatical subject; Genomic analysis

Jim Shaw's academic website.