List of tools frequently used while genome assembly
...10.1) CANU (v. 1.6) Unicycler (v. v0.4.1) Miniasm (v. 0.2-r137-dirty) I have used the following mappers minimap2 (v. 2.0rc1-r232) minimap (v. 0.2-r124-dirty) bwa...2075 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
...-vs-all read self-mappings (typically by minimap) as input and outputs an asse...out error correction. It also shows that minimap can be used as a read ov...e useful to produce high-quality assemblies. Minimap and miniasm are ultrafast too...2496 days ago
D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way
...ine tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation. We use minimap version 2 to align the two ge...2300 days ago
Alignment-free sequence comparison tools available for next-generation sequencing data analysis
...hs) Software (Python) http://github.com/cbib/MICADo General mapper Minimap Lightweight and fast read ma..., a special type of k-mers) Software (C) https://github.com/lh3/minimap Assembly De novo genome ass...2516 days ago
Run miniasm assembler on nanopore reads !
...-vs-all read self-mappings (typically by minimap) as input and outputs an asse...epeats: fq2fa ONT_A.fastq ONT_A.fasta minimap2 -xava-ont ONT_A.fasta ONT_A....">"$2"\n"$3}' > AONT_miniasm.fasta minimap2 -xasm10 AONT_miniasm.fasta A...2476 days ago
Install miniasm in Linux / Ubuntu
...he following additional packages will be installed: minimap The following NEW packages will be installed: miniasm minimap 0 upgraded, 2 newly installe...p://in.archive.ubuntu.com/ubuntu bionic/universe amd64 minimap amd64 0.2-3 [26.6 kB] Fetche...1695 days ago
dotPlotly: Generate an interactive dot plot from mummer or minimap alignments
Create an interactive dot plot from mummer output OR PAF format R script that makes a plotly interactive and/or static (png/pdf) dot plot. Shiny app available for testingTags: dotPlotly, Generate, interactive, dot, plot, mummer, minimap, alignments
2045 days ago
Comment on "Run miniasm assembler on nanopore reads !"
minimap2 –x ava-ont \ ../../trimming_practical/nan...anofilt/nanofilt_trimmed.fastq \ | gzip -1 > ./minimap.paf.gz miniasm -f \ ../...ing_practical/nanofilt/nanofilt_trimmed.fastq \ ./minimap.paf.gz > miniasm.gfa &n...942 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...w) for analyzing PacBio data. Minimap only accepts two FASTQ files...single file prior to running minimap. minimap2 -x ava-pb -t 23 \...cat.fastq /home/data/20170911_minimap2_pacbio_oly.paf > /home/da....fastq \ 20170918_oly_pacbio_minimap_mappings.paf \ 20170918_oly_...2313 days ago