MACS is an implementation of a ChIP-Seq analysis algorithm for identifying transcript factor binding sites named Model-based Analysis of ChIP-Seq (MACS). MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions and it improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation.

StringTie is a fast and efficient assembler of RNA-Seq sequence alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments of longer sequences that have been assembled from those reads. To identify differentially expressed genes between experiments, StringTie's output can be processed either by the Cuffdiff or Ballgown programs.

PRANK is a probabilistic multiple sequence alignment program for DNA, codon and amino-acid sequences. It is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. In addition, PRANK borrows ideas from maximum likelihood methods used in phylogenetics and correctly takes into account the evolutionary distances between sequences. Lastly, PRANK allows for defining a potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences.

Mantis is a space-efficient data structure that can be used to index thousands of raw-read genomics experiments and facilitate large-scale sequence searches on those experiments. Mantis uses counting quotient filters instead of Bloom filters, enabling rapid index builds and queries, small indexes, and exact results, i.e., no false positives or negatives. Furthermore, Mantis is also a colored de Bruijn graph representation, so it supports fast graph traversal and other topological analyses in addition to large-scale sequence-level searches.

Pando leverages multi-modal single-cell measurements to infer gene regulatory networks using a flexible linear model-based framework. By modeling the relationship between TF-binding site pairs with the expression of target genes, Pando simultaneously infers gene modules and sets of regulatory regions for each transcription factor.

Samtools implements various utilities for post-processing nucleotide sequence alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer.

The gdc-client provides several convenience functions over the GDC API which provides general download/upload via HTTPS.

A tiny C library for managing SOM (Self-Organizing Maps) neural networks.

This package provides an object for plotting GRanges, RleList, UCSC file formats, and ffTrack objects in multi-track panels.

The porechop package is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity. Porechop also supports demultiplexing of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR Barcoding Kit or Rapid Barcoding Kit.

This package provides a Python module creating/accessing GTF-based interval trees with associated meta-data. It is primarily used by the deeptools package.

This R tool infers, visualizes, and analyzes cell-cell communication networks. It supports scRNA-seq and spatially resolved transcriptomics data.

Bloom-filter-based error correction solution for high-throughput sequencing reads (BLESS) uses a single minimum-sized bloom filter is a correction tool for genomic reads produced by Next-generation sequencing (NGS). BLESS produces accurate correction results with much less memory compared with previous solutions and is also able to tolerate a higher false-positive rate. BLESS can extend reads like DNA assemblers to correct errors at the end of reads.

This package aims to simplify working with genomic region / interval data by providing a common interface that lets you access a wide selection of file types and formats for handling genomic region data---all using the same syntax.

PyEGA3 is a tool for viewing and downloading files from authorized EGA datasets. It uses the EGA data API and has several key features:

• Files are transferred over secure https connections and received unencrypted, so no need for decryption after download.

• Downloads resume from where they left off in the event that the connection is interrupted.

• Supports file segmenting and parallelized download of segments, improving overall performance.

• After download completes, file integrity is verified using checksums.

• Implements the GA4GH-compliant htsget protocol for download of genomic ranges for data files with accompanying index files.

python-cwl-upgrader is a standalone upgrader for CWL documents from version draft-3, v1.0, and v1.1 to v1.2.

CLIPper is a tool to define peaks in CLIP-seq datasets.

Bioinformaticians often have to convert sequence files between formats and do little manipulations on them, and it's not worth writing scripts for that. Seqmagick is a utility to expose the file format conversion in BioPython in a convenient way. Instead of having a big mess of scripts, there is one that takes arguments.

NanoSV is a software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies’ MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers.

CPAT is a method to distinguish coding and noncoding RNA by using a logistic regression model based on four pure sequence-based, linguistic features: ORF size, ORF coverage, Ficket TESTCODE, and Hexamer usage bias. Linguistic features based method does not require other genomes or protein databases to perform alignment and is more robust. Because it is alignment-free, it runs much faster and also easier to use.

SQUID is Sean Eddy's personal library of C functions and utility programs for sequence analysis.

This is an R package that integrates the installation of doublet-detection methods. In addition, this tool is used for execution and benchmark of those eight mentioned methods.

This package provides a VCF parser for Python.

Picard is a set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats. Picard is implemented using the HTSJDK Java library to support accessing file formats that are commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and VCF.