BOL

RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel...

a) bowtie2 mapping against host sequence Host example: human genome hg19 (download bowtie2 hg19 index)# 1) create bowtie2 index database (host_DB) from host reference genomebowtie2-build host_genome.fna host_DB# 2) bowtie2...

How to filter out host reads from paired-end fastq files?

Max 3' match

FlexiDot is a cross-platform dotplot suite generating high quality self, pairwise and all-against-all visualizations. To improve dotplot suitability for comparison of consensus and error-prone sequences, FlexiDot harbors routines for strict and...

Deeply conserved synteny resolves early events in vertebrate evolution https://www.nature.com/articles/s41559-020-1156-z #Synteny #Evolution #Vertebrate

Centre for Development of Advanced Computing (C-DAC) under the aegis of the National Supercomputing Mission (NSM), a Ministry of Electronics & Information Technology (MeitY) and Department of Science & Technology (DST) initiative, in...

Visualize genome in terminal https://asciigenome.readthedocs.io/en/latest/usage.html#quick-start #genome #visualisation

WEGO (Web Gene Ontology Annotation Plot) is a simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation results. As the GO vocabulary became more and more popular, WEGO was widely adopted and used in many...

Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1 https://www.nejm.org/doi/pdf/10.1056/NEJMc2004973 #corona #CoVID

CSAR-web is a web-based tool that allows the users to efficiently and accurately scaffold (i.e. order and orient) the contigs of a target draft genome based on a complete or incomplete reference genome from a related organism.  CSAR-web can...

Submit your SARS-CoV-2 sequence data to GenBank and SRA with our new submission landing page.

Dahak is a software suite that integrates state-of-the-art open source tools for metagenomic analyses. Tools in the dahak software suite will perform various steps in metagenomic analysis workflows including data pre-processing, metagenome assembly,...

IIT Delhi invites proposals for supercomputer-based COVID-19 research; Offers Rs 1 crore worth of computational time for FREE http://supercomputing.iitd.ac.in/ #IIT #Delhi #COVID #Free #SuperComputer

Extract the underscore separated values. $ awk '{split($0,a,"_"); print a[1]"_"a[2]}' aaa.txt | sort | uniq -u > all_ids_sm.txt #awk #bash #underscore #list

GeneSCF serves as command line tool for clustering list of genes based on functional annotation (Geneontology, KEGG, REACTOME and NCG). This tool requires gene list in the form of Entrez Gene IDs or Official gene symbols as a...

Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, Clark NR, Ma'ayan A. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics. 2013;128(14). http://amp.pharm.mssm.edu/Enrichr/

Basics commands for Docker https://www.digitalocean.com/community/tutorials/how-to-remove-docker-images-containers-and-volumes #Docker #commands

Data on protein-drug and protein-chemical interactions are rapidly accumulating in databases such as DrugBank and STITCH. These data usually reflect observed interactions, while the lack of data for a given protein-drug/chemical pair...

HiCanu, a significant modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering.  More...