Foldseek is a fast and sensitive command-line tool for comparing large protein structure datasets.
Read more
Tag: Bioinformatics
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.
Read more
SeqKit – manipulate FASTA and FASTQ files
SeqKit is a fast, cross-platform command-line toolkit for manipulating FASTA and FASTQ files.
Read more
MultiQC – aggregate results from bioinformatics analyses
MultiQC is a reporting tool that aggregates results from multiple bioinformatics analyses and samples into a single report
Read more
FastQC – quality control tool for high throughput sequence data
FastQC is a quality control tool for high throughput sequence data.
Read more
minimap2 – versatile sequence alignment program
minimap2 is a versatile sequence alignment program for genomic and spliced nucleotide sequences.
Read more
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.
Read more
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
Read more
samtools – manipulate next-generation sequencing data
samtools is a suite of tools written in C using HTSlib for manipulating next-generation sequencing data.
Read more
cramino – BAM/CRAM quality evaluation
cramino is a tool for quick quality assessment of cram and bam files, intended for long read sequencing.
Read more
GenomeTools – genome analysis software
The GenomeTools genome analysis system is a collection of bioinformatics tools (in the realm of genome informatics).
Read more
Genome Analysis Toolkit (GATK)
GATK is a genomic analysis toolkit focused on variant discovery.
Read more
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.
Read more
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.
Read more
mothur – analyze microbial communities
mothur fills the bioinformatics needs of the microbial ecology community. It’s software for describing and comparing microbial communities.
Read more
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.
Read more
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.
Read more
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.
Read more
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.
Read more
InterMine – integrate biological data sources
InterMine is a data warehouse system for the integration and analysis of biological data.
Read more