D-GENIES compares large genome assemblies with interactive dot plots, revealing sequence rearrangements, inversions and repeated regions.
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Tag: Bioinformatics
IGV-Web App – explore genomic data in a web browser
IGV-Web App lets researchers inspect reference genomes, alignments and variant tracks in a browser using local or remote genomic files.
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CGView.js – interactive circular and linear genome maps
CGView.js is a library for creating interactive circular and linear genome maps with features, plots and sequence-level navigation.
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SynFlow – visualize genome alignments and structural variation
SynFlow explores genome alignments, synteny and structural rearrangements with interactive multi-genome visualizations.
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Chromoscope – multiscale structural variation genome browser
Chromoscope is an interactive web genome browser for exploring structural variation and copy-number patterns across human cancer genomes.
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CDK – cheminformatics and bioinformatics toolkit
CDK is a Java toolkit providing algorithms and data structures for cheminformatics, molecular processing and chemical informatics.
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Foldseek – compare large protein structure datasets
Foldseek is a fast and sensitive command-line tool for comparing large protein structure datasets.
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Scanpy – scalable toolkit for analysing single-cell gene expression data
Scanpy is a scalable toolkit for analysing single-cell gene expression data. It can handle datasets containing more than one million cells.
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SeqKit – manipulate FASTA and FASTQ files
SeqKit is a fast, cross-platform command-line toolkit for manipulating FASTA and FASTQ files.
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MultiQC – aggregate results from bioinformatics analyses
MultiQC is a reporting tool that aggregates results from multiple bioinformatics analyses and samples into a single report
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FastQC – quality control tool for high throughput sequence data
FastQC is a quality control tool for high throughput sequence data.
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minimap2 – versatile sequence alignment program
minimap2 is a versatile sequence alignment program for genomic and spliced nucleotide sequences.
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BCFtools – variant calling and manipulating files in the Variant Call Format
BCFtools is a set of utilities for working with variant calls in Variant Call Format (VCF) and its binary counterpart BCF.
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SPAdes – versatile toolkit for assembling and analysing sequencing data
SPAdes is a versatile toolkit for assembling and analysing sequencing data. It is primarily developed for Illumina sequencing data
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samtools – manipulate next-generation sequencing data
samtools is a suite of tools written in C using HTSlib for manipulating next-generation sequencing data.
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HiGlass – interactive exploration of genomic contact maps
HiGlass visualises genomic contact matrices and sequencing tracks with linked views, continuous zooming and interactive comparisons.
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cramino – BAM/CRAM quality evaluation
cramino is a tool for quick quality assessment of cram and bam files, intended for long read sequencing.
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GenomeTools – genome analysis software
The GenomeTools genome analysis system is a collection of bioinformatics tools (in the realm of genome informatics).
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Genome Analysis Toolkit (GATK)
GATK is a genomic analysis toolkit focused on variant discovery.
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abPOA – adaptive banded Partial Order Alignment
abPOA is an extended version of Partial Order Alignment (POA) that performs adaptive banded dynamic programming (DP) with an SIMD implementation.
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