Popular software

Bioconda

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

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

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

ddRAGE

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


amplikyzer2

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


TaxMapper

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


warped

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


SimLoRD

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

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

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

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

PEAX

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


FlowG

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


MoSDi

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


StylPyl

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


SubSeqComb

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


Logomat-M

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