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

This package provides an implementation of run length arithmetic in Python using Cython. This is a support library for the pyranges stack.

This package provides utilities for exploratory analysis of large scale genetic variation data.

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

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

Succinct tree sequences are an efficient way of representing the genetic history - often technically referred to as an Ancestral Recombination Graph or ARG - of a set of DNA sequences.

The tree sequence format is output by a number of external software libraries and programs (such as msprime, SLiM, fwdpp, and tsinfer) that either simulate or infer the evolutionary ancestry of genetic sequences. This library provides the underlying functionality that such software uses to load, examine, and manipulate ARGs in tree sequence format, including efficientaccess to the correlated sequence of trees along a genome and general methods to calculate genetic statistics.

This package provides a library for reading BAM files quickly into dataframes in Python.

Vcztools provides a Python API to efficiently read VCZ data from local files and remote object stores using bcftools-compatible region and variant filtering syntax. It aims to provide a drop-in replacement for a subset of bcftools functionality.

This package contains a set of common Perl utilities for generating consistent Vcf headers. It primarily exists to prevent code duplication between some other projects.

The demes Python package provides an API for defining, parsing, and sharing Demes demographic models. Applications can use demes to parse human-readable Demes YAML files into fully-resolved demographic models. In addition, demes provides convenient data structures to simplify manipulation of demographic models.

This package provides a Python module to read and write the Newick format. In mathematics and phylogenetics, Newick tree format is a way of representing graph-theoretical trees with edge lengths using parentheses and commas.

hypothesis-vcf is designed to generate VCF files that conform to the VCF specification (version 4.3). It generates VCFs that are syntactically valid, but which don't have meaningful semantics.

Easel is an ANSI C code library developed by the Eddy/Rivas laboratory at Harvard. Easel supports our work on computational analysis of biological sequences using probabilistic models. Easel is used by HMMER, the profile hidden Markov model software that underlies several protein and DNA sequence family databases such as Pfam, and by Infernal, the profile stochastic context-free grammar software that underlies the Rfam RNA family database. Easel aims to make similar applications more robust and easier to develop, by providing a set of reusable, documented, and well-tested functions.

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).

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

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

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 python implementation of DESeq2.

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

This package computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller.

The carputils framework will be the optimal way to access openCARP for most users. This Python framework was developed to provide the means to easily encode in silico experiments including pre- and postprocessing. carputils will call the openCARP simulator.

This package is designed to help the scientist, engineer, statistician, etc., to construct appropriate experimental designs.