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 - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...
ccb.jhu.edu - StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length...
github.com - For a detailed description of the pipeline and how it integrates with other tools designed by the Aiden Lab see Genome Assembly Cookbook on http://aidenlab.org/assembly.
For the original version of the pipeline and to reproduce the...
github.com - HiCanu, a significant modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering.
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support.10xgenomics.com - Supernova generates phased, whole-genome de novo assemblies from a Chromium-prepared library.
Please see Achieving Success with De Novo Assembly and System Requirements before creating your Chromium libraries for...
lh3.github.io - Given a de novo assembly, we often measure the “average” contig length by N50. N50 is neither the real average nor median. It is the length of the contig such that this and longer contigs cover at least 50% of the assembly. A...
crossmap.sourceforge.net - CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)).
It supports most commonly...
easyfig.sourceforge.net - Easyfig has moved to github, for newer releases of Easyfig please visit our new webpage - https://mjsull.github.io/Easyfig. Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use...
bioinformatics.oxfordjournals.org - QUAST evaluates genome assemblies. For metagenomes, please see MetaQUAST project.It can works both with and without a given reference genome.The tool accepts multiple assemblies, thus is suitable for comparison.
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