Bio-vcf provides a DSL for processing the VCF format. Record named fields can be queried with regular expressions. Bio-vcf is a new generation VCF parser, filter and converter. Bio-vcf is not only very fast for genome-wide (WGS) data, it also comes with a filtering, evaluation and rewrite language and can output any type of textual data, including VCF header and contents in RDF and JSON.

Centrifuge is a microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. The system uses an indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.7 GB for all complete bacterial and viral genomes plus the human genome) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes.

Bowtie 2 is a fast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

Psupertime is supervised pseudotime for single cell RNAseq data. It uses single cell RNAseq data, where the cells have a known ordering. This ordering helps to identify a small number of genes which place cells in that known order. It can be used for discovery of relevant genes, for identification of subpopulations, and characterization of further unknown or differently labelled data.

The phylo module provides a biojava interface layer to the forester phylogenomics library for constructing phylogenetic trees.

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).

This package provides bioinformatic tools to align, deduplicate, reformat, filter and normalize DNA and RNA-seq data. It includes the following tools: BBMap, a short read aligner for DNA and RNA-seq data; BBNorm, a kmer-based error-correction and normalization tool; Dedupe, a tool to simplify assemblies by removing duplicate or contained subsequences that share a target percent identity; Reformat, to convert reads between fasta/fastq/scarf/fasta+qual/sam, interleaved/paired, and ASCII-33/64, at over 500 MB/s; and BBDuk, a tool to filter, trim, or mask reads with kmer matches to an artifact/contaminant file.

The SCDE package implements a set of statistical methods for analyzing single-cell RNA-seq data. SCDE fits individual error models for single-cell RNA-seq measurements. These models can then be used for assessment of differential expression between groups of cells, as well as other types of analysis. The SCDE package also contains the pagoda framework which applies pathway and gene set overdispersion analysis to identify aspects of transcriptional heterogeneity among single cells.

SnapTools can operate on snap files the following types of operations:

• index the reference genome before alignment;

• align reads to the corresponding reference genome;

• pre-process by convert pair-end reads into fragments, checking the mapping quality score, alignment and filtration;

• create the cell-by-bin matrix.

Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Typical use cases include:

1. mapping PacBio or Oxford Nanopore genomic reads to the human genome;

2. finding overlaps between long reads with error rate up to ~15%;

3. splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA reads against a reference genome;

4. aligning Illumina single- or paired-end reads;

5. assembly-to-assembly alignment;

6. full-genome alignment between two closely related species with divergence below ~15%.

This is a package for the discovery of communities in Pore-C concatemers.

This package provides an accurate VCF/GFF3/GTF LiftOver tool for new genome assemblies.

This is a package that lets you process UMI-4C data from scratch to produce nice plots.

This package provides several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable called bam.

This package provides Python bindings for spoa, a C++ implementation of the partial order alignment (POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which is used to generate consensus sequences

This package implements FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads.

PiGx is a collection of genomics pipelines. It includes the following pipelines:

• PiGx BSseq for raw fastq read data of bisulfite experiments

• PiGx RNAseq for RNAseq samples

• PiGx scRNAseq for single cell dropseq analysis

• PiGx ChIPseq for reads from ChIPseq experiments

All pipelines are easily configured with a simple sample sheet and a descriptive settings file. The result is a set of comprehensive, interactive HTML reports with interesting findings about your samples.

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). In addition to using one global graph FM (GFM) index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes, combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).

PySnpTools is a library for reading and manipulating genetic data. It can, for example, efficiently read whole PLINK *.bed/bim/fam files or parts of those files. It can also efficiently manipulate ranges of integers using set operators such as union, intersection, and difference.

RAxML is a tool for phylogenetic analysis and post-analysis of large phylogenies.

An ORF caller finds stretches of DNA that, when translated, are not interrupted by stop codons. OrfM finds and prints these ORFs.

LAMMPS is a classical molecular dynamics simulator designed to run efficiently on parallel computers. LAMMPS has potentials for solid-state materials (metals, semiconductors), soft matter (biomolecules, polymers), and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

t-Stochastic Neighborhood Embedding (t-SNE) is a highly successful method for dimensionality reduction and visualization of high dimensional datasets. A popular implementation of t-SNE uses the Barnes-Hut algorithm to approximate the gradient at each iteration of gradient descent. This package is a Cython wrapper for FIt-SNE.

This package implements two functions:

• pairwise.adonis is a wrapper function for multilevel pairwise comparison using adonis2 from package vegan. The function returns adjusted p-values using p.adjust(). It does not accept interaction between factors neither strata.

• pairwise.adonis2 accepts a model formula like in adonis from vegan. You can use interactions between factors and define strata to constrain permutations. For pairwise comparison a list of unique pairwise combination of factors is produced.