www.healthcare.uiowa.edu - Getting Started
These simple steps will help you integrate LSC into your transcriptomics analysis pipeline.
Read the LSC_requirements for running LSC.
Download and set-up the LSC package.
Follow the tutorial to see how...
github.com - Here is the command to run the tool:
python finisherSC.py destinedFolder mummerPath
If you are running on server computer and would like to use multiple threads, then the following commands can generate 20 threads to run FinisherSC.
python...
github.com - rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT)...
http://ani.mypathogen.cn/ - ANItools is a software package written by PERL scripts that can be run in a Linux/Unix system. If you want to compare bacterial genomes and calculate their average nucleotide identity (ANI), you could download and run this program directly. Or you...
github.com - Cogent is a tool that identifies gene families and reconstructs the coding genome using high-quality transcriptome data without a reference genome, and can be used to check assemblies for the presence of these known coding...
catchenlab.life.illinois.edu - Chromonomer is a program designed to integrate a genome assembly with a genetic map. Chromonomer tries very hard to identify and remove markers that are out of order in the genetic map, when considered against their local assembly order; and to...
github.com - Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a...
www.broadinstitute.org - VICUNA is a de novo assembly program targeting populations with high mutation rates. It creates a single linear representation of the mixed population on which intra-host variants can be mapped. For clinical samples rich in...
github.com - jumboDB tool for fast de Bruijn graph construction from long sequences (reads or genomes) with very low error rate. JumboDB is not a genome assembler by itself but rather a subroutine that translates a set of reads into compressed de Bruijn...
github.com - bacLIFE is a streamlined computational workflow that annotates bacterial genomes and performs large-scale comparative genomics to predict bacterial lifestyles and to pinpoint candidate genes, denominated lifestyle-associated genes (LAGs), and...
