Results for "NGS"
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KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler that allows to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number of biological conditions, and will quantify each...Tags: Bioinformatics, Analysis, NGS, KISSPLICE, Transcriptome, Assembler, Genome
2829 days ago
- methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods such as Agilent SureSelect methyl-seq. In addition, methylKit can deal ...
Tags: Bioinformatics, methylKit, Methylation, DNA, Analysis, Genome, NGS, Sequence
2903 days ago
- Reformat is a member of the BBMap/BBTools package. It is a multipurpose tool designed for converting reads or other nucleotide data between different formats. It supports, and can inter-convert: fastq fasta fasta+qual sam scarf (an old Illumina format) bam (if samtools is installed) gzip zip asc...
Tags: Bioinformatics, BBMap/BBTools package, Multipurpose, Tool, Converting, Formats, NGS
2724 days ago
- Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step Blaxter Lab, Institute of Evolutionary Biology, University of Edinburgh Goal: To create blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to...
Tags: Bioinformatics, Blobology, Blobplot, TAGC Plot, GC, Assembly, NGS, QC
2893 days ago
- The Genome Assembly Evaluation Metrics and Reporting (GAEMR) package is an assembly analysis framework composed a number of integrated modules. These modules can be executed as a single program to generate a complete analysis report, or executed individually to generate s...
Tags: Bioinformatics, GAEMR, Assembly, Stats, Correctness, Accuracy, Software, Tool, NGS
2893 days ago
CNIDARIA: fast, reference-free phylogenomic clustering
Motivation: Identification of biological specimens is a major requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying on prior knowledge, but these do not scale to arbitrarily large genomes and arbitrarily large phylogenetic distances. ...Tags: Bioinformatics, CNIDARIA, Fast, Reference-free, Phylogenomic, Clustering, NGS
2890 days ago
- In a nutshell Anvi’o is an analysis and visualization platform for ‘omics data. Please find the methods paper here: https://peerj.com/articles/1319/ Anvi’o would not have been possible without the help of many people who directly or indirectly contributed to its development. ...
Tags: Bioinformatics, Analysis, Visualization, Platform, Omics, NGS, Anvio
2890 days ago
How to extract 50% of the reads?
I would like to extract a subset of PE reads (50%) and store them in seperate files. It should be in both way "split by middle" or "random". Is there any way to achieve it?Tags: Reads, NGS, PE, Extract
2828 days ago
- I am doing megablast of a contig against NR database, but unable to understand this -outfmt '6 qseqid staxids qstart qend sstart send qseq sseq evalue length' Can you please help me to undestand all these.
Tags: Blastn, BLAST, Nucleotide, Alignment, Database, NR, Contig, NGS
2887 days ago
Linux command line exercises for NGS data processing
The purpose of this tutorial is to introduce students to the frequently used tools for NGS analysis as well as giving experience in writing one-liners. Copy the required files to your current directory, change directory (cd) to the linuxTutorial folder, and do all the processing inside: [uzi@qui...Tags: Bioinformatics, Tutorial, Genome, NGS, Pipelines
2885 days ago
