The preseq package is aimed at predicting and estimating the complexity of a genomic sequencing library, equivalent to predicting and estimating the number of redundant reads from a given sequencing depth and how many will be expected from additional sequencing using an initial sequencing experiment. The estimates can then be used to examine the utility of further sequencing, optimize the sequencing depth, or to screen multiple libraries to avoid low complexity samples.

This package analyses the Oxford Nanopore sequencing data at signal-level. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs (Single nucleotide polymorphisms) and indels with respect to a reference genome and more.

MethylDackel will process a coordinate-sorted and indexed BAM or CRAM file containing some form of BS-seq alignments and extract per-base methylation metrics from them. MethylDackel requires an indexed fasta file containing the reference genome as well.

gkm-SVM, a sequence-based method for predicting regulatory DNA elements, is a useful tool for studying gene regulatory mechanisms. LS-GKM is an effort to improve the method. It offers much better scalability and provides further advanced gapped k-mer based kernel functions. As a result, LS-GKM achieves considerably higher accuracy than the original gkm-SVM.

This package provides a C library for parsing local and remote BigWig files.

MUSIC is an algorithm for identification of enriched regions at multiple scales in the read depth signals from ChIP-Seq experiments.

This is a Python module for analyzing cell-hashing/nucleus-hashing data. It is the demultiplexing module of Pegasus, which is used by Cumulus in the demultiplexing step.

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.

Hclust2 is a handy tool for plotting heat-maps with several useful options to produce high quality figures that can be used in publications.

PAIRADISE is a method for detecting allele-specific alternative splicing (ASAS) from RNA-seq data. Unlike conventional approaches that detect ASAS events one sample at a time, PAIRADISE aggregates ASAS signals across multiple individuals in a population. By treating the two alleles of an individual as paired, and multiple individuals sharing a heterozygous SNP as replicates, PAIRADISE formulates ASAS detection as a statistical problem for identifying differential alternative splicing from RNA-seq data with paired replicates.

This package is intended to help users to efficiently analyze genomic data resulting from various experiments.

This is a C++ wrapper around the Tabix project which abstracts some of the details of opening and jumping in tabix-indexed files.

Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. It simply concatenates pieces of read sequences to generate the final unitig sequences. Thus the per-base error rate is similar to the raw input reads.

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

This package lets you read and write the PLINK BED format, simply and efficiently.

This helper package implements the HiCMatrix class for the HiCExplorer and pyGenomeTracks packages.

HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads. In addition to one global FM index that represents a whole genome, HISAT uses a large set of small FM indexes that collectively cover the whole genome. These small indexes (called local indexes) combined with several alignment strategies enable effective alignment of RNA-seq reads, in particular, reads spanning multiple exons.

This package aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot: bigwig, bed (many options), bedgraph, links (represented as arcs), and Hi-C matrices. pyGenomeTracks can make plots with or without Hi-C data.

This package is used for cell type identification in spatial transcriptomics. It also handles cell type-specific differential expression.

Pegasusio is a Python package for reading or writing single-cell genomics data.

Screed parses FASTA and FASTQ files and generates databases. Values such as sequence name, sequence description, sequence quality and the sequence itself can be retrieved from these databases.

IMP's broad goal is to contribute to a comprehensive structural characterization of biomolecules ranging in size and complexity from small peptides to large macromolecular assemblies, by integrating data from diverse biochemical and biophysical experiments. IMP provides a C++ and Python toolbox for solving complex modeling problems, and a number of applications for tackling some common problems in a user-friendly way.

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. This library provides population genetics-related modules.

This package is analyzing TCR and BCR sequences using unselected RNA sequencing data, profiled from fluid and solid tissues, including tumors. TRUST4 performs de novo assembly on V, J, C genes including the hypervariable CDR3 and reports consensus contigs of BCR/TCR sequences. TRUST4 then realigns the contigs to IMGT reference gene sequences to identify the corresponding gene and CDR3 details. TRUST4 supports both single-end and paired-end bulk or single-cell sequencing data with any read length.