BOL

http://www.festivalofgenomicslondon.com/ #biopharma #academia #healthcare #gemonics #ngs #omics

interleave fastq files https://gist.github.com/nathanhaigh/4544979 #interleave #fastq #pair #ngs #reads

Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3630013/ #Bacteria #NGS #Comparative #Genomics

Get the reads in fastq file: awk '{s++}END{print s/4}' file.fastq #reads #count #ngs #fastq

Find a pattern in first 7 characters of reads. bioawk -c fastx 'substr($seq,0,7) == $TAG { print }' reads.fq.gz #Reads #NGS #Extract #Pattern

All about #newbler #assembly https://contig.wordpress.com/ #NGS

Perl OneLiner http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/oneliners.html #Perl #Oneliner #NGS #Script

NGS onliner http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/subsetFASTAFASTAQ.html #OneLiner #NGS

Plotting nice coverage graph with R https://davetang.org/muse/2013/09/07/creating-a-coverage-plot-in-r/ #R #Plot #Coverage #NGS

Ion Torrent white paper: https://tools.thermofisher.com/content/sfs/manuals/CO25176_0512.pdf #NGS #Ion #Torrent #Steps

Assembly comparison https://github.com/WGLab/uniline/tree/master/src/assembly_comparison #NGS #Assembly #MUMMer

NGS tutorial http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/linux.html #NGS #Tutorial #Example

Genome and coverage https://rtsf.natsci.msu.edu/_rtsf/assets/File/depth%20and%20coverage.pdf #Coverage #Genome #Depth #Reads #NGS

Coverage R Plot http://davetang.org/muse/2013/09/07/creating-a-coverage-plot-in-r/ #R #Plot #Genome #Image #NGS #BAM

NGS exercise http://wiki.bits.vib.be/index.php/NGS_Exercise.5 #NGS #VIB #Training #Exercise