Comment on "poRe: an R package for the visualization and analysis of nanopore sequencing data"
...www.bioconductor.org/biocLite.R") biocLite("rhdf5") install.packages(c("shiny"...go get those: git clone https://github.com/mw55309/poRe_scripts.git We wi...Nick’s SQK-MAP-006 data are in the old FAST5 format so we use the script i...2237 days ago
Comment on "SPAdes hybrid genome assembly"
...o skip it. We will also only use 3 kmers to save time: ./SPAdes-3.6.2-Linux/bin/spades.py --only-assembler -t 4 -k 21,51,71 -1 SRR2627175_1.fastq.gz -2 SRR262...2237 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...e resulting assemblies are contiguous (i.e. long) but very noisy (i.e. full of errors) We start with an all against all comparison: minimap -Sw5 -L100 -m0 -t8 reads.fq reads....2238 days ago
Comment on "Basic command-line to run BLAST"
...lm.nih.gov (ftp.ncbi.nlm.nih.gov)... 130.14.250.12, 2607:f220:41e:250::7Connecting to ftp.ncbi.nlm...s) - ‘protein.fa.gz’ saved [12021576] urbe@urbo214b[Human_vs_Av...lm.nih.gov (ftp.ncbi.nlm.nih.gov)... 130.14.250.7, 2607:f220:41e:250::11Conn...2307 days ago
2315 days ago
Comment on "Important Journals, Blogs and Forums for Bioinformaticians"
Bioinformatics Research and Applications https://link.springer.com/book/10.1007/978-3-642-38036-5 Publish bioinformatics tools2320 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...nces[M::worker_pipeline::288.250*12.60] mapped 101108 sequenc...ine::1043.026*17.99] mapped 62540 sequences[M::worker_pipelin...line::2123.177*18.01] mapped 85392 sequences[M::worker_pipeli...uences[M::main] Version: 2.3-r531[M::main] CMD: minimap2 -xav...2344 days ago
Comment on "GraphMap - A highly sensitive and accurate mapper for long, error-prone reads"
...uence mapperGraphMap Version: v0.5.2Build date: Jun 6 2017 at 15:45:57 GraphMap (c) by Ivan S...normal and '-w overlap' modes). m5 - BLASR M5 format. [sam] -I,...alent to: '-a gotoh -w normal -M 5 -X 4 -G 8 -E 6' overlap - Equ...of the input read sequences. [0.45] -g, --max-regions INT If the...2355 days ago
Comment on "Venn Diagrams on R Studio"
Six-way Venn diagram https://stackoverflow.com/questions/32440128/nice-looking-five-sets-venn-diagrams2381 days ago
Comment on "Important Journals, Blogs and Forums for Bioinformaticians"
My collection of biology journals NatureNature GeneticsNature MedicineNature BiotechnologyNature Reviews GeneticsNature methodsNature CommunicationsBioin...2390 days ago