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Alignment-free sequence comparison tools available for next-generation sequencing data analysis
Last updated 3255 days ago by Abhimanyu Singh Comments (1)kallisto Transcript abundance quantification from RNA-seq data (uses pseudoalignment for rapid determination of read compatibility with targets) Software (C++) https://pachterlab.github.io/kallisto/ Sailfish Estimation of isoform abundances...
HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
By Rahul Nayak 3073 days agogithub.com - HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for...Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish...
By Jit 2814 days agogithub.com - Run a pipeline processing fast5s to a consensus in a single command. Recommended fixed "standard" and "fast" pipelines. Interchange basecaller, assembler, and consensus components of the pipelines simply by changing the target filepath. Seemless...ClinCNV: Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
By Neel 2454 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 749 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 2870 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...deepTools
By Martin Jones 4349 days agoUser-friendly tools for the normalization and visualization of deep-sequencing dataComputer simulation of genetic mechanism !!
By Jit 3859 days ago Comments (2)Computer simulation is the discipline of designing a model of an actual or theoretical physical/biological system, executing the model on a digital computer, and analyzing the execution output.cutadapt
By Radha Agarkar 3798 days agocutadapt.readthedocs.io - Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 3491 days agoStructural variation caller tools using long reads
