Software

GORAP

Genomewide ncRNA Annotation Pipeline

  • For automated non-coding RNA annotation, input: FASTA file(s)
  • Easy–Installer including all necessary software, libraries and up to date databases (Rfam, NCBI Taxonomy, Silva)
  • Based on BioPerl, Infernal, Blast, RNAmmer, tRNAscan, Bcheck, RAxML, CRT, Mafft, Samtools
  • Uses in-house filters (e.g. phylogeny based) and TPM/FPKM computation from BAM files
  • Offers RNome based phylogeny reconstruction
  • Root less installation for Linux, Unix
  • Requirements: Internet, gcc, wget, Perl, make
  • Source @GitHub
  • Alternative: Dockerfile for Linux/Windows/MacOS

PoSeiDon

Poseidon

Positive Selection Detection and Recombination Analysis

LRIscan

LRIscan a tool to predict conserved, genome-wide Long range RNA-RNA interactions
based on a multiple sequence alignment in only a few hours on an average computer.

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VrAP – Viral Assembly Pipeline

VrAP is based on the genome assembler SPAdes combined with a additional read correction and several filter steps. Our pipeline classifies the contigs to distinguish host from viral sequences by annotation and ORF density scores. With our new ORF density method we can identify viruses without any sequence homology to known references. We tested VrAP on real datasets generated with different sequencing technologies. We de novo identified new viruses representing new species and even genera and families.

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RNAgraphdist

  • Finds the shortest graph distance between to bases i and j
  • Handles thousands of input constraints
  • Plots all results with gnuplot
  • Optimized for multi-cores
  • Runtime complexity: O(n log n)
  • Download and Manual
  • Supplement

POMAGO

Multiple Genome Aligner

Designed for, but not limited to, bacterial genomes

SSRC

Split Sensitive Read Counter

For read counting and TPM calculation from mapping results, given an annotation file

  • Counts splitted reads only once
  • Counts strand specific
  • Counts parallelized
  • Input: BAM and GFF3/GTF
  • Output is GFF3 including TPM values
  • Requirements: Internet, g++, wget, Bash/sh, Perl, make
  • GitHub

Proteinortho

Orthology detection tool

  • Allows to detect orthologous proteins across hundreds of species
  • Small memory footprint
  • Optimized for multi-core and cluster environments
  • Runtime complexity: O(n2)
  • Download and Manual

Galculator

Nucleotide counter for fasta files

  • Counts mononucleotide frequencies, dinucleotide frequencies, and gapped dinucleotide frequencies (XnY)
  • Small constant memory footprint
  • Handles hundreds of petabytes if necessary
  • Runtime complexity: O(n)
  • Download and Manual

TR-PK-finder

Detects potential telomerase RNAs in fasta files