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ClinCNV: Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
By Neel 2332 days agogithub.com - ClinCNV detects CNVs in germline and somatic context in NGS data (targeted and whole-genome). We work in cohorts, so it makes sense to try ClinCNV if you have more than 10 samples (recommended amount - 40 since we estimate variances from...Figeno: Tool for plotting sequencing data along genomic coordinates.
By LEGE 627 days agogithub.com - Tool for plotting sequencing data along genomic coordinates. FIGENO is a FIGure GENerator for GENOmics With figeno, you can plot various types of sequencing data along genomic coordinates. Video...lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data
By BioJoker 2747 days agogithub.com - lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads...GATB : Genome Analysis Toolbox with de-Bruijn graph
By Jit 3690 days agohttps://gatb.inria.fr/ - The Genome Analysis Toolbox with de-Bruijn graph (GATB) provides a set of highly efficient algorithms to analyse NGS data sets. These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge...Bioinformatics tools and software
By Jit 3622 days agodrive5.com - USEARCH >Extreme high-throughput sequence analysis. Orders of magnitude faster than BLAST. MUSCLE >Multiple sequence alignment. Faster and more accurate than CLUSTALW. UPARSE >OTU clustering for 16S and other marker genes....FiNGS: Filters for Next Generation Sequencing
By Neel 1925 days agogithub.com - Key features Filters SNVs from any variant caller to remove false positives Calculates metrics based on BAM files and provides filtering not possible with other tools Fully user-configurable filtering (including which filters to use and their...Scallop: reference-based transcriptome assembler for RNA-seq
By Rahul Nayak 2950 days agogithub.com - Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts. Scallop achieves this improvement through a novel algorithm that can be...vcfR: a package to manipulate and visualize VCF data in R
By Jit 2780 days agogithub.com - VcfR is an R package intended to allow easy manipulation and visualization of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices from...Tools for RNA classification
By Abhi 1305 days ago Comments (1)The method used to isolate, enrich and sequence a sample will affect the composition of the sequencing data in terms of the types of RNA species represented and their relative abundances
