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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (317 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (773 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (934 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 (986 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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Musket: a multistage k-mer spectrum based corrector
By Jit 2693 days agomusket.sourceforge.net - Musket is a well-established leading next-generation sequencing read error correction algorithm targetting Illumina sequencing. This corrector employs the k-mer spectrum approach and introduces three correction techniques in a multistage...COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 2693 days agoftp.genomics.org.cn - An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE...HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
By Jit 2693 days agonservant.github.io - HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. Since version 2.7.0, HiC-Pro supports the main Hi-C protocols, including digestion protocols as well as protocols that do not...Bandage: interactive visualization of de novo genome assemblies
By Shruti Paniwala 2695 days agorrwick.github.io - Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes,...MetaSim A Sequencing Simulator for Genomics and Metagenomics.
By Jit 2695 days agoab.inf.uni-tuebingen.de - Our software can be used to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets. Based on a database of given genomes, the program allows the user to design a...MinION_GC: An R script to do some QC on MinION data
By Radha Agarkar 2696 days agogithub.com - Other tools focus on getting data out of the fastq or fast5 files, which is slow and computationally intensive. The benefit of this approach is that it works on a single, small, .txt summary file. So it's a lot quicker than most other things out...dnaPipeTE: de-novo assembly & annotation Pipeline for Transposable Elements
By Rahul Nayak 2697 days agogithub.com - dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs...PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
By Jit 2698 days agohttps://plast.inria.fr/ - PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms. Relying on unique software architecture,...collinearity: scripts to parse and analyse MCScanX collinearity output
By Jit 2700 days ago Comments (1)github.com - scripts to parse and analyse MCScanX collinearity outputScripts for the analysis of HGT in genome sequence data.
By Jit 2700 days agogithub.com - Scripts for the analysis of HGT in genome sequence data
