npScarf: Scaffolding and Completing Assemblies in Real-time Fashion
...pScarf (jsa.np.npscarf) is a program that scaffolds and completes draft genomes assemblies in real-time with Oxford Nanopore sequencing. The pipeline can run on a computing cluste...2529 days ago
Omega2: metagenome assembly pipeline
Omega found overlaps between reads using a prefix/suffix hash table. The overlap graph of reads was simplified by removing transitive edges and trimming short branches....2481 days ago
DIYA: a bacterial annotation pipeline for any genomics lab
DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV http://gmod.org/wiki/Diya2491 days ago
Unicycler: Hybrid assembly pipeline for bacterial genomes
Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets whe...(PacBio or Nanopore) where it runs a miniasm+Racon pipeline. For the best possible assemb...2358 days ago
DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication
We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation s...2354 days ago
Taxoblast : Taxoblast is a pipeline to identify contamination in genomic sequence
...tion of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interfa...ission of genomic data to public repositories. Our analysis pipeline is open-source and freely ava...2345 days ago
TULIP - The Uncorrected Long read Itegration Pipeline
#Running TULIP (The Uncorrected Long-read Integration Process), version 0.4 late 2016 (European eel) TULIP currently consists of to Perl scripts, tulipseed.perl and tul...2345 days ago
ONT assembly and Illumina polishing pipeline
This pipeline performs the following steps: Assembly of nanopore reads using Canu. Polish canu contigs using racon (optional). Map a paired-end Illumin...2345 days ago
RITA: Rapid identification of high-confidence taxonomic assignments for metagenomic data
...very high accuracy on short reads. Unlike other hybrid approaches which combine these predictions for all sequences to be classified, RITA uses a pipeline to first identify cases where...2341 days ago
dnaPipeTE: de-novo assembly & annotation Pipeline for Transposable Elements
dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is ver...2335 days ago