This package primarily exists to prevent code duplication between some other projects, specifically AscatNGS and Battenburg.

SHARC is a pipeline for somatic SV calling and filtering from tumor-only Nanopore sequencing data. It performs mapping, SV calling, SV filtering, random forest classification, blacklist filtering and SV prioritization, followed by automated primer design for PCR amplicons of 80-120 bp that are useful to track cancer ctDNA molecules in liquid biopsies.

This package provides procedures to calculate statistics for Oxford Nanopore sequencing data and alignments.

Framework for analyzing low-depth NGS data in heterogeneous/structured populations using PCA. Population structure is inferred by estimating individual allele frequencies in an iterative approach using a truncated SVD model. The covariance matrix is estimated using the estimated individual allele frequencies as prior information for the unobserved genotypes in low-depth NGS data.

The estimated individual allele frequencies can further be used to account for population structure in other probabilistic methods. pcangsd can be used for the following analyses:

• Covariance matrix

• Admixture estimation

• Inbreeding coefficients (both per-sample and per-site)

• HWE test

• Genome-wide selection scans

• Genotype calling

• Estimate NJ tree of samples

hiddenDomains is a suite of programs used to identify significant enrichment of ChIP-seq reads that span large domains, like HK27me3. The input data can be in BAM format, or in a tab-delimited 'reads per bin' format described below. The output is a BED formatted file the lists the enriched domains and their posterior probabilities.

Primer3 is a widely used program for designing PCR primers. PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.

MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets.

This packages provides a collection of small and efficient programs for performing some common and uncommon tasks with FASTQ files.

diemPy is a computational tool designed to polarize genomic data for hybrid zone analysis. The package implements an expectation-maximization (EM) algorithm to determine the optimal polarization of genetic markers, enabling researchers to identify and analyze patterns of introgression and hybridization in genomic datasets.

SHARC is a pipeline for somatic SV calling and filtering from tumor-only Nanopore sequencing data. It performs mapping, SV calling, SV filtering, random forest classification, blacklist filtering and SV prioritization, followed by automated primer design for PCR amplicons of 80-120 bp that are useful to track cancer ctDNA molecules in liquid biopsies.

The Spliced Transcripts Alignment to a Reference (STAR) software is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences.

This package provides a new way of computing bootstrap supports in large phylogenies.

This package provides in uncompressed version of the gnomAD structural variant sites.

SHARC is a pipeline for somatic SV calling and filtering from tumor-only Nanopore sequencing data. It performs mapping, SV calling, SV filtering, random forest classification, blacklist filtering and SV prioritization, followed by automated primer design for PCR amplicons of 80-120 bp that are useful to track cancer ctDNA molecules in liquid biopsies.

SeqAn is a C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. It contains algorithms and data structures for string representation and their manipulation, online and indexed string search, efficient I/O of bioinformatics file formats, sequence alignment, and more.

MetaMaps is tool specifically developed for the analysis of long-read (PacBio/Oxford Nanopore) metagenomic datasets.

This package contains the following programs: bamcollate2, bammarkduplicates, bammaskflags, bamrecompress, bamsort, bamtofastq.

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 3.

Anvi’o is a comprehensive platform that brings together many aspects of today’s computational strategies of data-enabled microbiology, including genomics, metagenomics, metatranscriptomics, pangenomics, metapangenomics, phylogenomics, and microbial population genetics in an integrated and easy-to-use fashion through extensive interactive visualization capabilities.

This package contains a collection of bioinformatics data structures and algorithms. It provides I/O classes, bitio classes, text indexing classes and BAM sequence alignment functionality.