Tool Library list page for genomics topic with tag 'Sequence analysis'



22 tools

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

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A tool that finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.

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Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.

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Multiple sequence alignment software. The name is occassionally spelled as ClustalOmega, Clustal Ω, ClustalΩ, Clustal O, ClustalO.

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Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.

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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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Collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

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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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program for filtering, converting and manipulating GFF files

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This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.

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High-performance visualization tool for interactive exploration of large, integrated datasets. It supports a wide variety of data types and format, including short-read alignments in the SAM/BAM format. Data can be viewed from local files or over the web via http.

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The igvtools utility provides a set of tools for pre-processing data files.

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MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.

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Refgenie manages storage, access, and transfer of reference genome resources. It provides command-line and Python interfaces to download pre-built reference genome "assets", like indexes used by bioinformatics tools. It can also build assets for custom genome assemblies. Refgenie provides programmatic access to a standard genome folder structure, so software can swap from one genome to another.

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This tool is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM, BAM and CRAM formats.

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This tool is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM, BAM and CRAM formats.

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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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A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.

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