Popular software


Bioconda Description: a distribution of bioinformatics software realized as a channel for the versatile package manager Conda; contains thousands of software packages (Homepage).
Author(s): Johannes Köster et al.


Snakemake Description: Python-like and make-like programming language for data analysis workflows, especially popular in genome-scale sequence analysis (Homepage).
Author(s): Johannes Köster & Sven Rahmann


Cutadapt Description: a tool for cutting adapters from sequencing datasets with many additional features such as quality trimming, demultiplexing, etc. (Homepage).
Author(s): Marcel Martin

Recent software


hackgap Description: a tool for counting gapped k-mers (Homepage).
Author(s): Jens Zentgraf & Sven Rahmann


ting Description: a tool for clustering large scale T cell receptor repertoires by antigen-specificity (Homepage).
Author(s): Felix Mölder & Sven Rahmann


xengsort Description: an ultrafast lightweight and accurate tool for xenograft sorting, using 3-way bucketed Cuckoo hashing (Homepage).
Author(s): Jens Zentgraf & Sven Rahmann


TreeLas Description: two efficient fused lasso solvers for tree graphs; an implementation of the SEA 2020 paper by Elias Kuthe and Sven Rahmann (Homepage).
Author(s): Elias Kuthe


Cuckopt Description: a tool to calculate a cost-optimal assignment of elements in multi-way bucketed Cuckoo hash tables; this provides an implementation of the method of the ALENEX 2020 paper by Jens Zentgraf, Henning Timm and Sven Rahmann. (Homepage).
Author(s): Jens Zentgraf & Sven Rahmann


amplikyzer2 Description: an analysis tool for amplicon bisulfite sequencing that features automatic allele sorting; can also analyze NOMe-seq data (Homepage).
Author(s): Marcel Bargull, Sven Rahmann


ddRAGE Description: A simulation tool for ddRAD-seq datasets that can produce a detailed and annotated ground truth for the evaluation of analysis pipelines and software. (Homepage).
Author(s): Henning Timm & Sven Rahmann


TaxMapper Description: a database, workflow and an analysis tool for reliably mapping sequenced datasets to a provided microeukaryotic reference (Homepage).
Research project: Metatranscriptomics
Author(s): Daniela Beisser, Henning Timm & Sven Rahmann


SimLoRD Description: a read simulator for third generation sequencing reads focused on the Pacific Biosciences SMRT error model (Homepage).
Author(s): Bianca Stöcker, Johannes Köster & Sven Rahmann


betamix Description: a tool that robustly estimates a mixture of one-dimensional beta distributions to given datapoints in the interval [0,1]; motivated by the need to describe methylation level distributions. (Homepage).
Author(s): Christopher Schröder & Sven Rahmann


dupre Description: a tool to estimate the duplicate rate of a sequencing library at an arbitrarysequencing depth, when the occupancy vector of a (small) subsample is known; useful for deciding decide which coverage to aim for, weighing new discoveries vsersus cost. (Homepage).
Research project: Diversity
Author(s): Christopher Schröder & Sven Rahmann


dinopy Description: a DNA input and output library for Python, providing readers and writers for FASTA and FASTQ files, along with support for samtools faidx files, and generators for solid and gapped q-grams (k-mers). (Homepage).
Author(s): Henning Timm & Till Hartmann

Older software


Description: methods for (DNA) motif statistics, e.g. to compute the exact occurrence count distribution of a motif, exact motif discovery, extraction of motifs with provably optimal p-value, analysis of pattern matching algorithms (to compute, for given algorithm and pattern, the exact distribution of the number of character accesses caused by searching a random text). (Homepage).
Research project: Paas
Author(s): Tobias Marschall


Description: a web based frontend for argparse that allows launching and running python programs through a web browser. (Homepage).
Author(s): Christoph Stahl


Description: a collection of fully automated peak extraction methods for MCC/IMS datasets, provided as a modular extensible framework backed by an open source implementation. (Homepage).
Author(s): Marianna D'Addario, Dominik Kopczynski & Sven Rahmann


Description: a proof-of-concept implementation of flowgram-string alignment as described in our GCB 2013 paper “Aligning Flowgrams to DNA Sequences” (Homepage).
Author(s): Marcel Martin & Sven Rahmann


Description: command line utility that scans a text or tex input file for patterns that indicate bad writing style (e.g., according to Strunk and White's classic "The Elements of Style") and reports occurrences of these, together with suggestions for improvement. Beta version. Retired. (Homepage).
Author(s): Sven Rahmann


Description: Java classes for subsequence combinatorics. The Java class SubsequenceCombinatorics implements the algorithms described in our research project on subsequence combinatorics. The Java class SubsequenceCombinatoricsTest is a JUnit based test and at the same time demonstrates the use of the routines in SubsequenceCombinatorics.java. Documentation in html form is also included in the archive. In order to make the classes work on your system, you may have to change its package declaration. (Homepage).
Research project: Subsequencecombinatorics
Author(s): Sven Rahmann


Description: a server for generating HMM logos, a generalization of sequence logos, using stack width for visualizing insertion/deletion probabilities; now retired. (Homepage).
Author(s): Benjamin Schuster-Böckler & Sven Rahmann

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