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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 (624 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (785 days ago): Sequencing coverage is defined as the average number of reads that covers...
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MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via...
By Jit 2201 days agogithub.com - MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to...SKESA: strategic k-mer extension for scrupulous assemblies
By Jit 2201 days agogithub.com - SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit shows that SKESA produces assemblies that have high sequence quality and contiguity,...ANItools web: a web tool for fast genome comparison within multiple bacterial strains
By Jit 2201 days agohttp://ani.mypathogen.cn/ - ANItools is a software package written by PERL scripts that can be run in a Linux/Unix system. If you want to compare bacterial genomes and calculate their average nucleotide identity (ANI), you could download and run this program directly. Or you...sim3C: Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)
By Jit 2202 days agogithub.com - Required python modules biopython intervaltree numpy scipy tqdm PyYAMLPacasus: Correction of palindromes in long reads from PacBio and Nanopore
By BioStar 2203 days agogithub.com - Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification. Check the poster from the Revolutionizing Next-Generation Sequencing (2nd edition) conference in the source...ASCIIGenome: genome browser based on command line interface and designed for running from console...
By Neel 2206 days ago Comments (2)github.com - ASCIIGenome is a genome browser based on command line interface and designed for running from console terminals. Since ASCIIGenome does not require a graphical interface it is particularly useful for quickly visualizing genomic data...BamView: a free interactive display of read alignments in BAM data files
By Neel 2206 days agobamview.sourceforge.net - To run the application on UNIX from the downloaded jar file run the UNIX: java -mx512m -jar BamView.jar and extra command line options are given when '-h' is used: java -jar BamView.jar -h BAM files can be specified on the command line with the...AMStat: display statistics of large sequence files from next generation sequencing projects
By Neel 2206 days agosamstat.sourceforge.net - SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to SAM/BAM files all statistics are reported for unmapped, poorly and accurately mapped reads...pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks
By Neel 2206 days agogithub.com - pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot: bigwig bed (many options) bedgraph links (represented as arcs) Hi-C matrices (if HiCExplorer is...MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other...
By Neel 2210 days agogithub.com - An increasing number of studies are mapping protein binding and nucleotide modifications sites throughout the transcriptome. Often, these sites cluster in certain regions of the transcript, giving clues to their function. Hence, it is informative to...
