Comment on "Estimate Genome Size"
# count k-mers (see jellyfish documentation for options) gzip -dc reads1.fastq.gz reads2.fastq.gz | jellyfish count -m 31...e estimate_genome_size.pl --kmer=31 --peak=42 --fastq=reads1.fastq.gz reads2.fastq.gz1940 days ago
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2165 days ago
Comment on "Installing Perl environment on Linux"
...ors/id/Y/YA/YANICK/Parallel-ForkManager-1.19.tar.gz ... OKConfiguring Parallel-Fo...cpan.org/authors/id/B/BI/BIGJ/Test-Warn-0.36.tar.gz ... OKConfiguring Test-Warn-0....org/authors/id/C/CM/CMUNGALL/Data-Stag-0.14.tar.gz ... OKConfiguring Data-Stag-0...2168 days ago
Comment on "poRe: an R package for the visualization and analysis of nanopore sequencing data"
...oaded, and back at the Linux command line: R CMD INSTALL poRe_0.16.tar.gz The fastq extraction scrip...wget http://spades.bioinf.spbau.ru/release3.6.2/SPAdes-3.6.2-Linux.tar.gz gunzip < SPAdes-3.6.2-Lin...2216 days ago
Comment on "SPAdes hybrid genome assembly"
...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 SRR2627175_2.fastq.gz --nanopore minion.pa...2216 days ago
2217 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 assemble...2217 days ago
Comment on "Perl Module Installation"
tar zxf Digest-SHA1-2.13.tar.gz cd Digest-SHA1-2.13 perl Makefile.PL make make test make install2280 days ago
Comment on "Basic command-line to run BLAST"
...mo_sapiens/protein/protein.fa.gz => ‘protein.fa.gz&rs.... done.==> SIZE protein.fa.gz ... 12021576==> PASV ... d...a/data/Adineta_vaga.v2.pep.fa.gzResolving www.genoscope.cns.fr.... done.==> SIZE protein.fa.gz ... 10463933==> PASV ... d...2286 days ago