github.com - Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly...
github.com - MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome...
github.com - MitoHiFi v3.2 is a python pipeline distributed under MIT License !
MitoHiFi was first developed to assemble the mitogenomes for a wide range of species in the Darwin Tree of Life Project...
github.com - Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). The software is currently alpha level, feel free to use and report issues encountered.
Canu is...
code.google.com - splitbam splits a BAM by chromosomes.
Using the reference sequence dictionary (*.dict), it also creates some empty BAM files if no sam record was found for a chromosome. A pair of 'mock' SAM-Records can also be added to those empty BAMs to...
github.com - DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies
Our work is published in Scientific Reports:
Ye, C. et al. DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous...
github.com - Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm uses an A-Bruijn graph to find the overlaps between reads and does not require them to be error-corrected. After...
github.com - A comparative genome scaffolding tool based on MUMmer
mScaffolder scaffolds a genome using an existing high quality genome as the reference. It aligns the two genomes using nucmer utility from MUMmer and then orders and orients the contigs of the...
github.com - GRSR is a Tool for Deriving Genome Rearrangement Scenarios for Multiple Uni-chromosomal Genomes. This tool will do the following steps:
Step 1. Run mugsy to get multiple sequence alignment results.
Step 2 & 3. Extraction of the Coordinates...
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...