ALLHiC: Phasing and scaffolding polyploid genomes based on Hi-C data
...we developed a new Hi-C scaffolding pipeline, called ALLHIC, specifically tailored to the polyploid genomes. ALLHIC pipeline contains a total of 5 steps: prune, partition,&...1979 days ago
BlobToolKit: A toolkit for genome assembly QC
...rmat used by BlobTools2 and the Viewer. The BlobToolKit Pipeline is a configurable Snakemake pipeline that automates all steps from retrieving public datase...1551 days ago
DeepHiC: A Generative Adversarial Network for Enhancing Hi-C Data Resolution
...based model for enhancing Hi-C data resolution. We developed this server for helping researchers to enhance their own low-resolution data by a few steps of clicks. Ab initio training...1540 days ago
Dahak: benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.
...software suite that integrates state-of-the-art open source tools for metagenomic analyses. Tools in the dahak software suite will perform various steps in metagenomic analysis workf...1503 days ago
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
...nd voting-based classification of the entire contig / MAG based on classification of the individual ORFs. CAT and BAT can be run from intermediate steps if files are formated appropr...1464 days ago
sunbeam: A robust, extensible metagenomics pipeline
Sunbeam is a pipeline written in snakemake that simplifies and automates many of the steps in metagenomic sequencing analysis. It uses conda to manage dependencie...1433 days ago
GROMACS: a versatile package to perform molecular dynamics
...the world. The server is furthermore aimed to provide a user friendly and efficient MD experience by performing many preparation and optimization steps automatically. GROMACS conda...1383 days ago
SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins
...l automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta...re using a web interface. Internal checks for the assembly and binning steps inform about the consistency...1373 days ago
CRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and Ka/Ks in R
...nalysis pipeline in R (R Core Team, 2019). It reimplements the Conditional Reciprocal Best Hit (CRBH) algorithm crb-blast and covers all necessary steps from sequence similarity sear...1286 days ago
Caretta – A multiple protein structure alignment and feature extraction suite
...lication and additionally outputs an aligned structure feature matrix for a given set of input structures, which can readily be used in downstream steps for supervised or unsupervise...1250 days ago