BOL

BAM2BED conversion bamToBed -i overall_exp_genome_rep1.bam > alignment.bed #Bed #bam #bamToBed #convert

Machine Learning books https://semanti.ca/blog/?the-most-important-machine-learning-books #books #machine #learn

Check the file systems and sizes. $ df --block-size=G #Linux #Size #df

Next generation error correction https://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=6104&context=etd #Error #Correct #NGS #Algorithms

Generate consensus from BAM file samtools mpileup -uf chr5B_leaf_rust.fasta M27454_5B_reads_sorted.bam | bcftools call -c | vcfutils.pl vcf2fq #BAM #Consensus

Consensus of nucleotide sequences https://www.perlmonks.org/bare/?node_id=500962 #Consensus #Nucleotide #DNA

PacBio data to download http://www.cbcb.umd.edu/software/PBcR/original/index.html #pacbio #data

https://www.ebi.ac.uk/about/news/announcements/25-genomes-UK-species #Genomes #Sequenced #UK

https://pb-falcon.readthedocs.io/en/latest/quick_start.html#quick-start #Falcon-Unzip #Genome #Assembly

https://blog.rstudio.com/2018/10/05/r2d3-r-interface-to-d3-visualizations/ #r2d3 #visualization

Mapping subreads https://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/SubreadUsersGuide.pdf #R

#SSPACE Basic, SSAKE-based #Scaffolding of Pre-Assembled Contigs after Extension https://github.com/nsoranzo/sspace_basic

#BLASTCLUST - BLAST score-based single-linkage #clustering. http://nebc.nerc.ac.uk/bioinformatics/documentation/blast/blastclust.html

#Mappy provides a convenient #interface to #minimap2, a fast and accurate #C program to #align #genomic and transcribe nucleotide #sequences. https://pypi.org/project/mappy/

GATK is open source https://software.broadinstitute.org/gatk/ #GATK #Broad