Results for "assemble"
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Comment on "Short-read assembly using Spades !"
SPAdes (St. Petersburg genome assembler) is a popular tool for short-read assembly. It can assemble reads generated from Illumina, Ion...ir> with the name of the output directory where the assembled contigs will be saved. Ch...429 days ago
- ...ersion] [-citation] \ [-correct | -trim | -assemble | -trim-assemble] \ [-s <assembly-specifica...cted reads -trim - generate trimmed reads -assemble - generate an assembly -trim-...f the haploid genome size of what is being assembled. It is used primarily to est...
2108 days ago
Comment on "poRe: an R package for the visualization and analysis of nanopore sequencing data"
...fastq extraction scripts for poRe are in github, so let’s go get those: git clone https://github.com/mw55309/poRe_scripts.git We will assemble using SPAdes, so let’s...2183 days ago
Comment on "SPAdes hybrid genome assembly"
use SPAdes to assemble the data. SPAdes is a swiss-army knife of genome assembly tools, a...y use 3 kmers to save time: ./SPAdes-3.6.2-Linux/bin/spades.py --only-assembler -t 4 -k 21,51,71...2183 days ago
- ...updated version of the Celera assembler that was used to assemble th...[-correct | -trim | -assemble | -trim-assemble] \...three stages (correct, trim, assemble) are computed. To compute...s in order: Correct Trim Assemble By default canu runs these...
2184 days ago
Comment on "Run miniasm assembler on nanopore reads !"
I followed this to assemble the genome using ONT (nanopore reads) Minimap and miniasm are ultrafast...-m0 -t8 reads.fq reads.fq | gzip -1 > reads.paf.gz Then we can assemble miniasm -f reads.fq read...2184 days ago
- ...*** Platanus is a de novo assembler designed to assemble high-throughput data. It can...NOPSIS ***** > platanus assemble -f PE.fa 2>ass_log.txt &g...PREFIX_contig.fa : assembled contiguous sequences...PREFIX_scaffold.fa : assembled sequences that include gaps(...
2808 days ago
Comment on "Software packages for next gen sequence analysis"
DNAMAN uses fast alignment algorithms to assemble quickly and accurately a large number of overlapping sequences. This could be a nice tutorial for genome assemblies with overlapping sequences http://www.lynnon.com/pc/assembly.html3248 days ago
