KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts. The fol...columns in a matrix produced by the "comp". In addition, KAT contains a python...1978 days ago
FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
Here is the command to run the tool: python finisherSC.py destinedFolder mummerPath If you are running on server comp...ads, then the following commands can generate 20 threads to run FinisherSC. python...2082 days ago
Snakemake—a scalable bioinformatics workflow engine
Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow.2068 days ago
2036 days ago
sim3C: Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)
Required python modules biopython intervaltree numpy scipy tqdm PyYAML1997 days ago
pWhatsHap: a parallel, high-performance version of WhatsHap
Given the potential relevance of efficient haplotyping in several analysis pipelines, we have designed and engine...on of WhatsHap. pWhatsHap is embedded in a toolkit developed in Python...1996 days ago
1938 days ago
NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads
NxRepair is a python module that automatically detects large structural errors in de novo assemblies using Nextera mate pair reads. The decector will break a contig at...1925 days ago
UpSetR: An R Package for the Visualization of Intersecting Sets and their Properties
UpSetR generates static UpSet plots. The UpSet technique visualizes set intersections in a matrix layout...tR shiny app. Here is the source code for the shiny wrapper. A Python...1920 days ago
1672 days ago