The HH-suite is a software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).

This package provides version 1.12 of the HTSlib C library for high-throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib.

This package contains some tools for processing BAM files including:

• bamsormadup: parallel sorting and duplicate marking

• bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name

• bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field

• bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column

• bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading.

• bamsort: reads BAM and writes BAM resorted by coordinates or query name

• bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name.

This package provides tools for dealing with Unique Molecular Identifiers (UMIs) and Random Molecular Tags (RMTs) in genetic sequences. There are six tools: the extract and whitelist commands are used to prepare a fastq containing UMIs +/- cell barcodes for alignment. The remaining commands, group, dedup, and count/count_tab, are used to identify PCR duplicates using the UMIs and perform different levels of analysis depending on the needs of the user.

Entrez Direct (EDirect) is a method for accessing the National Center for Biotechnology Information's (NCBI) set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a terminal. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.

EDirect also provides an argument-driven function that simplifies the extraction of data from document summaries or other results that are returned in structured XML format. This can eliminate the need for writing custom software to answer ad hoc questions.

This package provides a set of R functions to parse markdown and other generic helpers.

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.

VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.

Biopython is a set of tools for biological computation including parsers for bioinformatics files into Python data structures; interfaces to common bioinformatics programs; a standard sequence class and tools for performing common operations on them; code to perform data classification; code for dealing with alignments; code making it easy to split up parallelizable tasks into separate processes; and more.

MafFilter is a program dedicated to the analysis of genome alignments. It parses and manipulates MAF files as well as more simple fasta files. This package can be used to design a pipeline as a series of consecutive filters, each performing a dedicated analysis. Many of the filters are available, from alignment cleaning to phylogeny reconstruction and population genetics analysis. Despite various filtering options and format conversion tools, MafFilter can compute a wide range of statistics (phylogenetic trees, nucleotide diversity, inference of selection, etc.).

BioJava is a project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.

This package provides the core libraries.

The goal of anpan is to consolidate statistical methods for strain analysis. This includes automated filtering of metagenomic functional profiles, testing genetic elements for association with outcomes, phylogenetic association testing, and pathway-level random effects models.

ChIPKernels is an R package for building different string kernels used for DNA Sequence analysis. A dictionary of the desired kernel must be built and this dictionary can be used for determining kernels for DNA Sequences.

Scallop is a reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts.

This package provides a library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.8+).

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.

This package provides a toolkit for measuring and comparing ATAC-seq results. It was written to make it easier to spot differences that might be caused by ATAC-seq library prep or sequencing. The main program, ataqv, examines aligned reads and reports some basic metrics.

NGS is a domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. The API itself is independent from any particular back-end implementation, and supports use of multiple back-ends simultaneously.

BioRuby comes with a comprehensive set of Ruby development tools and libraries for bioinformatics and molecular biology. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO.

Implementation of the Smith-Waterman algorithm.

gffcompare is a tool that can:

1. compare and evaluate the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie);

2. collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g. resulted from assembly of different samples);

3. classify transcripts from one or multiple GTF/GFF3 files as they relate to reference transcripts provided in a annotation file (also in GTF/GFF3 format).

pySCENIC is a Python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

This library implements an efficient loopless multiset combination generation algorithm which is (approximately) described in "Loopless algorithms for generating permutations, combinations, and other combinatorial configurations.", G. Ehrlich - Journal of the ACM (JACM), 1973. (Algorithm 7.)

SeqGL is a group lasso based algorithm to extract transcription factor sequence signals from ChIP, DNase and ATAC-seq profiles. This package presents a method which uses group lasso to discriminate between bound and non bound genomic regions to accurately identify transcription factors bound at the specific regions.