Latest comments
Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (168 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (625 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (786 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 (838 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
Tag cloud
Bioinformatics, Genome, NGS, assembly, Analysis, tool, reads, Sequencing, Data, alignment, Sequence, Visualization, R, Pipeline, Computational Biology, Genomics, genomes, Annotation, Long, Tools, Tutorial, Software, Fast, Gene, DNA, Plot, sequences, Genomic, Assemblies, PacBio, Package, Assembler, de novo, Synteny, Learn, read, Chromosome, accurate, Interactive, Perl, nanopore, genes, Program, Web, Scaffolding, Database, Server, Python, Mapping, Comparative
Our Sponsors
All site bookmarks
Synteny Portal: a web-based application portal for synteny block analysis
By Jit 2741 days agobioinfo.konkuk.ac.kr - Synteny Portal, a versatile web-based application portal for constructing, visualizing and browsing synteny blocks. With Synteny Portal, users can easily (i) construct synteny blocks among multiple species by using prebuilt alignments in the UCSC...Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator
By Jit 2741 days agosourceforge.net - Grinder is a versatile program to create random shotgun and amplicon sequence libraries based on DNA, RNA or proteic reference sequences provided in a FASTA file. Grinder can produce genomic, metagenomic, transcriptomic, metatranscriptomic,...AVID: A Global Alignment Program
By Archana Malhotra 2741 days agowww.ncbi.nlm.nih.gov - A new global alignment method called AVID. The method is designed to be fast, memory efficient, and practical for sequence alignments of large genomic regions up to megabases long. We present numerous applications of the method, ranging from the...SuRankCo: supervised ranking of contigs in de novo assemblies
By Neel 2741 days agosourceforge.net - SuRankCo is a machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which...SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology
By Abhimanyu Singh 2742 days agoufmg-simba.sourceforge.net - SIMBA, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS)...GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.
By Abhimanyu Singh 2742 days agogithub.com - GRASS (GeneRic ASsembly Scaffolder)-a novel algorithm for scaffolding second-generation sequencing assemblies capable of using diverse information sources. GRASS offers a mixed-integer programming formulation of the contig scaffolding problem, which...npScarf: Scaffolding and Completing Assemblies in Real-time Fashion
By Jit 2742 days agogithub.com - npScarf (jsa.np.npscarf) is a program that scaffolds and completes draft genomes assemblies in real-time with Oxford Nanopore sequencing. The pipeline can run on a computing cluster as well as on a laptop computer for microbial datasets. It...BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic...
By Jit 2743 days agogithub.com - This tool is for users to upgrade their metagenomics assemblies using long reads. This includes fixing mis-assemblies and scaffolding/gap-filling. If you encounter any issues, please contact me at kklam@eecs.berkeley.edu. My name is Ka-Kit...Finishing !!
By Jit 2744 days agowww.cbcb.umd.edu - The process of finishing a genome and moving it from a draft stage (the result of sequencing and initial assembly) to a complete genome is typically a time and resource intensive task. The advent of new sequencing technologies...Pollux: platform independent error correction of single and mixed genomes
By Jit 2746 days agogithub.com - Pollux: General-purpose error corrector that corrects errors introduced by Illumina, Ion Torrent, and Roche 454 sequencing technologies and can be applied to single- or mixed-genome data. In addition to correcting substitution errors, we locate and...
