Rahul Nayak
A Bioinformatician
Latest comments
- Neel on CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (836 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
- Neel on CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (836 days ago): CheckM for...
- Rahul Nayak on CrossMap: program for genome coordinates conversion between different assemblies (1031 days ago): https://www.researchgate.net/publication/357925950_FastRemap_A_Tool_for_Quickly_...
- Rahul Nayak on RGFA: powerful and convenient handling of assembly graphs (1767 days ago): The Graphical Fragment Assembly (GFA) is a proposed format which allow to...
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Genome, Assembly, reads, analysis, NGS, de novo, Tools, Bioinformatics, tool, visualization, data, R, sequencing, Pipeline, Computational Biology, Long, Assemblies, fast, AligNment, annotation, assembler, genomes, Software, MUltiple, Python, genes, database, Genomics, Tutorial, Education, scaffolding, transcriptome, Nanopore, fastq, Perl, Merging, Solution, Tree, Network, Resolution, U-Plot, gene, Bacteria, gap, Genomic, structure, Elements, mapping, Suite, system
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Rahul Nayak's bookmarks
Snakemake Tutorials !
By Rahul Nayak 927 days agocarpentries-incubator.github.io - A lesson introducing the Snakemake workflow system for bioinformatics analysis. Prerequisites This is an intermediate lesson and assumes learners have already done some bioinformatics: Familiarity with the BASH command shell, including...MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer...
By Rahul Nayak 939 days agogithub.com - MUM&Co is able to detect:Deletions, insertions, tandem duplications and tandem contractions (>=50bp & <=150kb)Inversions (>=1kb) and translocations (>=10kb)PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index
By Rahul Nayak 945 days agogithub.com - PuffAligner, a fast, accurate and versatile aligner built on top of the Pufferfish index. PuffAligner is able to produce highly sensitive alignments, similar to those of Bowtie2, but much more quickly. While exhibiting similar speed to the ultrafast...Understanding HiFi Reads !
By Rahul Nayak 973 days agopacb.com - While little public data is available for either of the new synthetic long read approaches, Illumina showed an example comparison earlier this year at the Festival of Genomics & Biodata conference (FoG 2022). In the IGV screenshot...Tiara: deep learning-based classification system for eukaryotic sequences
By Rahul Nayak 983 days agoacademic.oup.com - With a large number of metagenomic datasets becoming available, eukaryotic metagenomics emerged as a new challenge. The proper classification of eukaryotic nuclear and organellar genomes is an essential step toward a better understanding of...kebabs: package provides functionality for kernel based analysis of biological sequences via...
By Rahul Nayak 994 days agowww.bioinf.jku.at - The kebabs package provides functionality for kernel based analysis of biological sequences via Support Vector Machine (SVM) based methods. Biological sequences include DNA, RNA, and amino acid (AA) sequences. Sequence kernels define...SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files
By Rahul Nayak 997 days agotelatin.github.io - A general-purpose program to manipulate and parse information from FASTA/FASTQ files, supporting gzipped input files. Includes functions to interleave and de-interleave FASTQ files, to rename sequences and...Comparative Genomics Workshops !
By Rahul Nayak 1031 days agowww.genome.gov - This meeting's objective was to obtain a big picture look at the current state of the field of comparative genomics with a focus on commonalities across genomic investigations into humans, model organisms (both traditional and...CrossMap: program for genome coordinates conversion between different assemblies
By Rahul Nayak 1031 days ago Comments (1)crossmap.sourceforge.net - CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats...HIV genome database !
By Rahul Nayak 1035 days agowww.hiv.lanl.gov - HIV resources https://www.hiv.lanl.gov/components/sequence/HIV/search/search.html
