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sudo apt-get install libgd-svg-perl to install GD::SVG #Perl #Linux #Install #Graph #Plot

Scripts required to calculate tetramer frequencies and create input files for ESOM https://github.com/tetramerFreqs/Binning #Bin #Tetramer

Steps for #Prokaryotic #genome #assembly and #annotation http://www.edamamecourse.org/docs/metagenome_assembly_and_annotation.html

Understanding #Overlap Layout #Consensus #assembly http://www.cs.jhu.edu/~langmea/resources/lecture_notes/assembly_olc.pdf #OLC #Assembly

Nice R graphs http://christophergandrud.github.io/networkD3/

#Clustering metagenomic #contigs on #tetranucleotide frequency http://cgat.readthedocs.io/en/latest/recipes/metagenome_contigs_kmers.html

Convert a SAM file to tab-delimited alignment coordinates https://gist.github.com/sjackman/7016520 #SAM #BAM #Convert #Tab

Understanding MegaBlast https://gordonlab.wustl.edu/btheta/blast/docs/megablast_readme.html #Blast #BLASTn #MegaBlast #Alignment

Whole-Genome Sequencing (WGS) PPT http://www.bx.psu.edu/~ratan/Sequence%20Analysis.pdf #PPT #WGS #Ratan

SAM flags https://broadinstitute.github.io/picard/explain-flags.html #SAM #Flags

Remove all blank lines from file. perl -i.bak -n -e "print if /\S/" ../finalSample.fa #Perl #Tricks #PerlOneliner

SAM and BAM handling with Perl http://search.cpan.org/~lds/Bio-SamTools/lib/Bio/DB/Sam.pm # Perl #SAM #BAM

#Download #blastDB #locally. $ wget "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.*.tar.gz" for NT and wget "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.*.tar.gz" for NR

Split the bam file by chromosome. $ bamtools split -in file.bam -reference #Split #Bam #Bamtools

#Contiguous and #accurate de novo #assembly of #metazoan genomes with modest long read coverage https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw654