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 f...2087 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.2073 days ago
sim3C: Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)
Required python modules biopython intervaltree numpy scipy tqdm PyYAML2002 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 a...2001 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 t...1930 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 p...1925 days ago
1677 days ago
Gooey: Turn (almost) any Python command line program into a full GUI application with one line
Turn (almost) any Python command line program into a full GUI application with one line The easiest way to install...ctory git clone https://github.com/chriskiehl/Gooey.git run setup.py python s...1649 days ago
1645 days ago
Seq: A high-performance, Pythonic language for bioinformatics
Seq is a programming language for computational genomics and bioinformatics. With a Python-compatible syntax and a host of domain-specific features and o...writing high-performance genomics software as easy as writing Python c...1627 days ago