This package provides tools for filtering on quality and/or read length, and optional trimming after passing filters. Reads from stdin, writes to stdout. Optionally reads directly from an uncompressed file specified on the command line. It is intended to be used directly after fastq extraction, prior to mapping, or in a stream between extraction and mapping.

Biosoup is a C++ collection of header-only data structures used for storage and logging in bioinformatics tools.

The IQ-TREE software was created as the successor of IQPNNI and TREE-PUZZLE (thus the name IQ-TREE). IQ-TREE was motivated by the rapid accumulation of phylogenomic data, leading to a need for efficient phylogenomic software that can handle a large amount of data and provide more complex models of sequence evolution. To this end, IQ-TREE can utilize multicore computers and distributed parallel computing to speed up the analysis. IQ-TREE automatically performs checkpointing to resume an interrupted analysis.

As input IQ-TREE accepts all common sequence alignment formats including PHYLIP, FASTA, Nexus, Clustal and MSF. As output IQ-TREE will write a self-readable report file (name suffix .iqtree), a NEWICK tree file (.treefile) which can be visualized by tree viewer programs such as FigTree, Dendroscope or iTOL.

Key features of IQ-TREE:

• Fast and effective stochastic algorithm to reconstruct phylogenetic trees by maximum likelihood;

• An ultrafast bootstrap approximation (UFBoot) to assess branch supports;

• An ultrafast and automatic model selection (ModelFinder);

• A flexible simulator (AliSim) which can simulate sequence alignments under more realistic models than Seq-Gen and INDELible;

• Several fast branch tests like SH-aLRT and aBayes test and tree topology tests like the approximately unbiased (AU) test.

This package provides IQ-TREE version 2.

IGoR is a C++ software designed to infer V(D)J recombination related processes from sequencing data such as:

• Recombination model probability distribution

• Hypermutation model

• Best candidates recombination scenarios

• Generation probabilities of sequences (even hypermutated)

Its heavily object oriented and modular style was designed to ensure long term support and evolvability for new tasks in assessing TCR and BCR receptors features using modern parallel architectures.

This package provides a phylogeny dating method using least-squares algorithms and criteria.

This package provides a tool to extract assembly statistics from FASTA and FASTQ files.

MCView creates a Shiny app facilitating interactive exploration and annotation of Metacell models.

The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

CMAPLE is a C++ reimplementation of MAPLE - a novel likelihood-based phylogenetic inference method for pandemic-scale epidemiological genomic data.

This package provides a tool to download or view data in the cloud environments of ICGC.

Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm, which is used to generate consensus sequences. It supports three alignment modes: local (Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment (overlap), and three gap modes: linear, affine and convex (piecewise affine).

FastQC aims to provide a QC report which can spot problems which originate either in the sequencer or in the starting library material. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.

This package is used to apply filtering on raw VCF calls generated using CaVEMan.

This package provides the reference implementation of CGP workflow for CaVEMan SNV analysis.

This package contains functions to extract information from Oxford Nanopore sequencing data and alignments.

CAT and BAT are pipelines for the taxonomic classification of long DNA sequences and MAGs of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. CAT and BAT can be run from intermediate steps if files are formated appropriately.

Primer3-py is a Python-abstracted API for the popular Primer3 library. The intention is to provide a simple and reliable interface for automated oligo analysis and design.

Primer3-py also includes bindings for the Primer3 primer design engine if you’d prefer to use an established pipeline. The IO parameters mirror those of the original Primer3, but you don’t have to deal with messy and slow file IO for your automated workflows.

scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and analysis of single-cell omics data, built on top of PyTorch and AnnData.

This package provides a python implementation of DESeq2.