FastQC is a quality control tool for high throughput sequence data.
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Tag: Bioinformatics
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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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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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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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 – high-performance visualization tool for interactive exploration of large, integrated genomic datasets
The Integrative Genomics Viewer is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
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InterMine – integrate biological data sources
InterMine is a data warehouse system for the integration and analysis of biological data.
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UGENE – bioinformatics software
UGENE is a cross-platform set of integrated bioinformatics software integrating well-known biological tools and algorithms.
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BioJava – Java framework for bioinformatics
BioJava is a project dedicated to providing Java tools for processing biological data.
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bedtools – powerful toolset for genome arithmetic
The bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks.
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EMBOSS – software analysis package for molecular biology
EMBOSS is The European Molecular Biology Open Software Suite developed for the needs of the molecular biology (e.g. EMBnet) user community.
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