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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (214 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (671 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (832 days ago): Sequencing coverage is defined as the average number of reads that covers...
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VCFtools: perform common tasks with VCF files such as file validation, file merging, intersecting,...
By Rahul Nayak 2347 days agovcftools.sourceforge.net - VCFtools contains a Perl API (Vcf.pm) and a number of Perl scripts that can be used to perform common tasks with VCF files such as file validation, file merging, intersecting, complements, etc. The Perl tools support all versions of the VCF...AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
By Jit 2347 days agowww.healthcare.uiowa.edu - Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser...NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data
By Jit 2347 days agogithub.com - NextSV, a meta SV caller and a computational pipeline to perform SV calling from low coverage long-read sequencing data. NextSV integrates three aligners and three SV callers and generates two integrated call sets (sensitive/stringent) for different...gSearch: a fast and flexible general search tool for whole-genome sequencing
By Jit 2347 days agoml.ssu.ac.kr - gSearch compares sequence variants in the Genome Variation Format (GVF) or Variant Call Format (VCF) with a pre-compiled annotation or with variants in other genomes. Its search algorithms are subsequently optimized and implemented in a...Fastq stats in Emoji :)
By Rahul Nayak 2348 days agogithub.com - Read one or more FASTQ files, fastqe will compute quality stats for each file and print those stats as emoji... for some reason. Given a fastq file in Illumina 1.8+/Sanger format, calculate the mean (rounded) score for each position and...LSC :a long read error correction tool
By Jit 2352 days agowww.healthcare.uiowa.edu - Getting Started These simple steps will help you integrate LSC into your transcriptomics analysis pipeline. Read the LSC_requirements for running LSC. Download and set-up the LSC package. Follow the tutorial to see how...REVIGO: Reduced Visualize gene ontology
By Jit 2354 days agohttp://revigo.irb.hr/ - REViGO can take long lists of Gene Ontology terms and summarize them by removing redundant GO terms. The remaining terms can be visualized in semantic similarity-based scatterplots, interactive graphs, or tag clouds. More about...nanofilt: Filtering and trimming of long read sequencing data
By Jit 2355 days ago Comments (1)github.com - Filtering on quality and/or read length, and optional trimming after passing filters.Reads from stdin, writes to stdout. Intended to be used: directly after fastq extraction prior to mapping in a stream between extraction and...GFinisher: a new strategy to refine and finish bacterial genome assemblies
By Jit 2359 days agogfinisher.sourceforge.net - GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/scaffolds with genomes references. java -Xms2G -Xmx4G -jar...ARC: pipeline which facilitates iterative, reference guided de novo assemblies
By Jit 2359 days agoibest.github.io - ARC is a pipeline which facilitates iterative, reference guided de novo assemblies with the intent of: Reducing time in analysis and increasing accuracy of results by only considering those reads which should assemble...
