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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (172 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (628 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (789 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 (842 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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Jabba: Hybrid Error Correction for Long Sequencing Reads
By Jit 2518 days agogithub.com - Jabba is a hybrid error correction tool to correct third generation (PacBio / ONT) sequencing data, using second generation (Illumina) data. Input Jabba takes as input a concatenated de Bruijn graph and a set of sequences: the de Bruijn graph...Seal: SEquence ALignment evaluation suite
By Jit 2520 days agocompbio.case.edu - Seal is a comprehensive sequencing simulation and alignment tool evaluation suite. This software (implemented in Java) provides several utilities that can be used to evaluate alignment algorithms, including: Reading a pre-existing reference...JPred4: A Protein Secondary Structure Prediction Server
By Poonam Mahapatra 2525 days agowww.compbio.dundee.ac.uk - JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure...3d-dna: 3D de novo assembly (3D DNA) pipeline
By Jit 2526 days agogithub.com - This code is designed to enable anyone to reproduce the Hs2-HiC and the AaegL4 genomes reported in: Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 2017. Unless otherwise...Rectangle Graph for Repeat Resolution in Genome Assembly
By Rahul Nayak 2526 days agobioinf.spbau.ru - Ultimate tool for resolving repeats in genome assemblies. Though the specific implementation of the idea of the rectangle graph approach is already included into the current SPAdes distribution, we're also releasing the Rectangle Graph Module...CAMSA :: a tool for Comparative Analysis and Merging of Scaffold Assemblies
By Rahul Nayak 2526 days agohttps://cblab.org/camsa/ - CAMSA – is a tool for Comparative Analysis and Merging of Scaffold Assemblies, distributed both as a standalone software package and as Python library under the MIT license. Main features: works with any number of...xmatchview: smith-waterman alignment visualization
By Rahul Nayak 2526 days agogithub.com - xmatchview and xmatchview-conifer are imaging tools for comparing the synteny between DNA sequences. It allows users to align 2 DNA sequences in fasta format using cross_match and displays the alignment in a variety of image formats. xmatchview and...Ra assembler - a de novo DNA assembler for third generation sequencing data
By biogeek 2527 days agogithub.com - Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS). Ra is in...Recovery of complete genomes from metagenomes
By Jit 2528 days agomadsalbertsen.github.io - This project contains scripts and tutorials on how to assemble individual microbial genomes from metagenomes, as described in: Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes Mads...Magic-BLAST: a tool for mapping large next-generation RNA or DNA sequencing runs against a whole...
By Jit 2528 days agoncbi.github.io - Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of...
