Comment on "Installing Salmon for Trinity !"
Sometime, you need to provide the path ➜ Tools git:(master) ✗ PATH=$PATH:/home/tools/anaconda3/bin ➜ Tools git:(master) ✗ export $PATH2186 days ago
2196 days ago
Comment on "Run miniasm assembler on nanopore reads !"
Must read paper https://genome.cshlp.org/content/27/5/737.full2226 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...sp;in the code below) for analyzing PacBio data. Minimap only accept...ap2 -x ava-pb -t 23 \ 20170911_oly_pacbio_cat.fastq \ 20170911_oly...sm \ -f \ /home/data/20170911_oly_pacbio_cat.fastq /home/data/2017...niasm_reads.fasta 20170905_minimap2_pacibio_oly.paf > 20170918_mi...2226 days ago
Comment on "poRe: an R package for the visualization and analysis of nanopore sequencing data"
...tor.org/biocLite.R") biocLite("rhdf5") install.packages(c("shiny","bit64","data...5309/poRe_scripts.git We will assemble using SPAdes, so let’s go get tha...old_format/extract2D MAP006-1/MAP006-1_downloads/pass/ > minion.pass.2D.fastq...2233 days ago
Comment on "SPAdes hybrid genome assembly"
use SPAdes to assemble the data. SPAdes is a swiss-army knife of genome assembly t...ill also only use 3 kmers to save time: ./SPAdes-3.6.2-Linux/bin/spades.py...2627175_2.fastq.gz --nanopore minion.pass.2D.fastq -o SPAdes...2233 days ago
2233 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...but very noisy (i.e. full of errors) We start with an all against all comparison: minimap -Sw5 -L100 -m0 -t8 reads.fq reads.fq | gzip -1 > reads.paf.gz Then we can assemb...2233 days ago
2240 days ago
Comment on "List of genome announcement, notes and reporting journals"
Genomics data also accept draft genome assembly papers https://www.sciencedirect.com/journal/genomics-data2241 days ago