Sickle is a tool that trims reads based on quality and length thresholds. It uses sliding windows to detect low-quality bases at the 3'-end and high-quality bases at the 5'-end. Additionally, it discards reads based on the length threshold.

This package provides graphical user interfaces to organize and visualize Nanopore sequencing data.

This package provides a Python environment for phylogenetic tree exploration.

The goal of bedtorch is to provide a fast BED file manipulation tool suite native in R.

Newick-utils is a suite of utilities for processing phylogenetic trees in Newick format. Functions include re-rooting, extracting subtrees, trimming, pruning, condensing, drawing (ASCII graphics or SVG).

Megahit is a fast and memory-efficient NGS assembler. It is optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single-cell assembly.

DIAMOND is a BLAST-compatible local aligner for mapping protein and translated DNA query sequences against a protein reference database (BLASTP and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short reads at a typical sensitivity of 90-99% relative to BLAST depending on the data and settings.

This library implements a FASTA and a FASTQ parser without relying on a complex dependency tree.

This library contains the genomics components of the Bio++ phylogenetics library. It is part of the Bio++ project.

The SRA Toolkit from NCBI is a collection of tools and libraries for reading of sequencing files from the Sequence Read Archive (SRA) database and writing files into the .sra format.

CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.

TADbit is a complete Python library to deal with all steps to analyze, model, and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models.

Pando leverages multi-modal single-cell measurements to infer gene regulatory networks using a flexible linear model-based framework. By modeling the relationship between TF-binding site pairs with the expression of target genes, Pando simultaneously infers gene modules and sets of regulatory regions for each transcription factor.

HTSlib is a C library for reading/writing high-throughput sequencing data. It also provides the bgzip, htsfile, and tabix utilities.

This package implements the custom CRAM codecs used for "EXTERNAL" block types. These consist of two variants of the rANS codec (8-bit and 16-bit renormalisation, with run-length encoding and bit-packing also supported in the latter), a dynamic arithmetic coder, and custom codecs for name/ID compression and quality score compression derived from fqzcomp.

This program searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, the AdapterRemoval may be used to recover a consensus adapter sequence for paired-ended data, for which this information is not available.

PRINSEQ is a bioinformatics tool to help you preprocess your genomic or metagenomic sequence data in FASTA or FASTQ formats. The tool is written in Perl and can be helpful if you want to filter, reformat, or trim your sequence data. It also generates basic statistics for your sequences.

Millefy is a tool for visualizing read coverage of scRNA-seq(single-cell RNA sequencing) datasets in genomic contexts. By dynamically and automatically reorder single cells based on locus-specific pseudo time, Millefy highlights cell-to-cell heterogeneity in read coverage of scRNA-seq data.

Anglemania extracts genes from multi-batch scRNA-seq experiments for downstream dataset integration. It improves conventional usage of highly-variable genes for integration tasks.

This package is a rasterization preprocessing framework that aggregates cellular information into spatial pixels to reduce resource requirements for spatial omics data analysis. SEraster reduces the number of points in spatial omics datasets for downstream analysis through a process of rasterization where single cells gene expression or cell-type labels are aggregated into equally sized pixels based on a user-defined resolution. SEraster can be incorporated with other packages to conduct downstream analyses for spatial omics datasets, such as detecting spatially variable genes.

This framework facilitates the execution of differential junction usage (DJU) methods. Additionally, it enables the integration of results from multiple DJU methods.

BioRuby comes with a comprehensive set of Ruby development tools and libraries for bioinformatics and molecular biology. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO.

This package implements the method csSAM that computes cell-specific differential expression from measured cell proportions using SAM.

MultiQC is a tool to aggregate bioinformatics results across many samples into a single report. It contains modules for a large number of common bioinformatics tools.