Tool Library list page for genomics topic with tag 'Sequencing'



29 tools

BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.

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BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.

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Bowtie is an ultrafast, memory-efficient short read aligner.

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Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

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Find and remove 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 3’ sequencing adapter because the read is longer than the molecule that is sequenced. Amplicon reads start with a primer sequence. Poly-A tails are useful for pulling o

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This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier

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Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using

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This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larg

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This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larg

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The Genome Analysis Toolkit (GATK) is a set of bioinformatic tools for analyzing high-throughput sequencing (HTS) and variant call format (VCF) data. The toolkit is well established for germline short variant discovery from whole genome and exome sequencing data. GATK4 expands functionality into copy number and somatic analyses and offers pipeline scripts for workflows. Version 4 (GATK4) is ope

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The Genome Analysis Toolkit (GATK) is a set of bioinformatic tools for analyzing high-throughput sequencing (HTS) and variant call format (VCF) data. The toolkit is well established for germline short variant discovery from whole genome and exome sequencing data. GATK4 expands functionality into copy number and somatic analyses and offers pipeline scripts for workflows. Version 4 (GATK4) is ope

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The Genome Analysis Toolkit (GATK) is a set of bioinformatic tools for analyzing high-throughput sequencing (HTS) and variant call format (VCF) data. The toolkit is well established for germline short variant discovery from whole genome and exome sequencing data. GATK4 expands functionality into copy number and somatic analyses and offers pipeline scripts for workflows. Version 4 (GATK4) is ope

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Identify and quantify DNA damage patterns in ancient DNA.

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MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.

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Nanopore sequence read simulator based on statistical characterization.

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Disambiguating two species in next generation sequencing data from grafted samples. Operates on DNA or RNA-seq alignments to the two species and separates the components at very high sensitivity and specificity.

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A set of command line tools for manipulating high-throughput sequencing (HTS) data in formats such as SAM/BAM/CRAM and VCF. Available as a standalone program or within the GATK4 program.

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Add or Replace Read Groups in an input BAM or SAM file.

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This package is aimed at predicting and number of distinct reads and how many will be expected from additional sequencing using an initial sequencing experiment. The estimates can then be used to examine the utility of further sequencing, optimize the sequencing depth, or to screen multiple libraries to avoid low complexity samples.

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This package is aimed at predicting and number of distinct reads and how many will be expected from additional sequencing using an initial sequencing experiment. The estimates can then be used to examine the utility of further sequencing, optimize the sequencing depth, or to screen multiple libraries to avoid low complexity samples.

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Tool to trim primers of multiplex deep sequencing data.

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Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.

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A software package with various utilities for processing alignments in the SAM format, including variant calling and alignment viewing.

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The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.

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The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.

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Subread is a general-purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. It uses a new mapping paradigm called "seed-and-vote" to achieve fast, accurate and scalable read mapping. It automatically determines if a read should be globally or locally aligned, therefore particularly powerful in mapping RNA-seq reads. It supports indel detection and can map reads

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A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.

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VarScan, an open source tool for variant detection that is compatible with several short read align-ers.

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