BOL

Pacbio pipeline http://www.cbcb.umd.edu/software/PBcR/ #Pacbio #Reads #Pipeline

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

Reads QC http://evomicsorg.wpengine.netdna-cdn.com/wp-content/uploads/2015/01/introQC.pdf #Quality #Reads #NGS

#Extract #Chromosome #Number And Start Position #Reads: samtools view bamfile.bam|awk '{print $3 "\t" $4 "\t" $4+length($10)-1}' > newfile.tab

#Extract all #Reads from #BAM file for a #region Chr10:18000-45500 using #samtools: samtools view input.bam "Chr10:18000-45500" > output.bam

#Mapping #sequencing #reads to a #reference #genome with #Bowtie2: a step-by-step guide https://insidedna.me/tutorials/view/how-to-use-bowtie2-read-mapping

Reference-free Prediction of Rearrangement Breakpoint Reads http://bioinformatics.oxfordjournals.org/content/early/2014/05/28/bioinformatics.btu360.short #Reference #Breakpoint #Reads #Rearrangement

Assemble short reads http://ged.msu.edu/angus/tutorials/short-read-assembly.html #Tutorial #ABySS #Bacteria #Reads #Assembly #Genomics #NGS