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.gz1925 days ago
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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...2153 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...2202 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...2202 days ago
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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...2203 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 install2266 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...2272 days ago