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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (200 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (657 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (818 days ago): Sequencing coverage is defined as the average number of reads that covers...
- Neel on CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (870 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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Comparative genomics visualisation tools !
By Neel 1043 days agocmdcolin.github.io - Comparative genomics visualisation tools !chromeister: An ultra fast, heuristic approach to detect conserved signals in extremely large...
By Jit 1057 days agogithub.com - chromeister: An ultra fast, heuristic approach to detect conserved signals in extremely large pairwise genome comparisons. USAGE: -query: sequence A in fasta format -db: sequence B in fasta format -out: output matrix -kmer Integer: k>1...GenomeTools: The versatile open source genome analysis software
By Neel 1058 days agohttp://genometools.org/ - The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named...odgi: optimized dynamic genome/graph implementation
By Abhimanyu Singh 1058 days agogithub.com - odgi provides an efficient and succinct dynamic DNA sequence graph model, as well as a host of algorithms that allow the use of such graphs in bioinformatic analyses. Careful encoding of graph entities allows odgi to efficiently...Comparative Genomics Workshops !
By Rahul Nayak 1065 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 1065 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 1070 days agowww.hiv.lanl.gov - HIV resources https://www.hiv.lanl.gov/components/sequence/HIV/search/search.htmlVCF Compare !
By Rahul Nayak 1072 days agowiki.bits.vib.be - compare two BWA mapping methods with the online hg18-mapped data We first operate a rapid inspection of the different BAM files using samtools flagstat. Illumina provided chr21 read mapping obtained with their GA IIx deep...oGNM:Conformational dynamics based on contact topology in a coarse-grained presentation
By Abhi 1074 days agodyn.life.nthu.edu.tw - Gaussian Network Model (GNM) is a powerful tool to sample conformational dynamics based on contact topology in a coarse-grained presentation. Here we present a method to consider protein dynamics in the presence of ‘environment’ (1). The...MimiLook: A Phylogenetic Workflow for Detection of Gene Acquisition in Major Orthologous Groups of...
By Abhi 1081 days agopubmed.ncbi.nlm.nih.gov - This tool detects statistically validated events of gene acquisitions with the help of the T-REX algorithm by comparing individual gene tree with NCBI species tree. In between the steps, the workflow decides about handling paralogs, filtering...
