cramino is a tool for quick quality assessment of cram and bam files, intended for long read sequencing.
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Tag: Bioinformatics
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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AliView – alignment viewer and editor
AliView is an alignment viewer and editor for bioinformatics that aims to be one of the fastest and most intuitive to use.
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mothur – analyze microbial communities
mothur fills the bioinformatics needs of the microbial ecology community. It’s software for describing and comparing microbial communities.
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MUSCLE – multiple sequence and structure alignment
MUSCLE aligns biological sequences and protein structures, generates alternative alignments and helps assess phylogenetic robustness.
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SeaView – graphical sequence alignment and phylogenetic analysis
SeaView provides graphical DNA and protein sequence alignment, phylogenetic tree construction and evolutionary analysis on Linux.
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Apollo – collaborative genome annotation editor
Apollo provides collaborative genome annotation with real-time editing, annotation history, ontology terms and shared JBrowse views.
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Artemis – genome viewer and annotation editor
Artemis provides sequence annotation, six-frame translation, comparative genomics and graphical inspection of genomic features.
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JBrowse – scalable genome browser
JBrowse is a scalable genome browser for exploring local and remote genomic tracks, alignments, variants and annotations on the desktop.
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Integrated Genome Browser – genomic data visualisation
Integrated Genome Browser explores sequencing reads, gene models, expression signals and genome annotations with animated zoom and plugins.
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Genome Workbench – genomic data analysis
Genome Workbench combines sequence and alignment viewing, phylogenetic trees, BLAST results and locally organised research data.
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Tablet – sequence assembly and alignment viewer
Tablet displays sequence assemblies, read alignments, coverage and genomic features with paired-end viewing and searchable read data.
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Ensembl Genome Browser – explore genomic data and annotations
Ensembl helps researchers explore genes, transcripts, genomic regions and annotations across thousands of species in an interactive browser.
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Genome Data Viewer – explore annotated genome assemblies
Genome Data Viewer explores annotated genome assemblies with interactive tracks, gene searches, BLAST alignments and custom genomic data.
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Bioconductor – tools for the analysis and comprehension of high-throughput genomic data
Bioconductor is a software project which provides tools for the analysis and comprehension of high-throughput genomic data.
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Biopython – tools for biological computation written in Python
Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.
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BioPerl – computational molecular biology tools
BioPerl is a collection of Perl tools for computational molecular biology used by large and small academic laboratories, and pharmaceuticals.
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Integrative Genomics Viewer – genomic data visualisation
IGV explores genome alignments, variants, coverage, gene annotations and other large datasets through fast, interactive desktop tracks.
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