BOL

#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

Reverse complement of fasta sequence $ tr -d "\n " < chrII.fa | tr "[ATGCatgcNn]" "[TACGtacgNn]" | rev > chrII_reverseHai.fa #Reverse #Complement #DNA

Add some text at the beginning of the file $ echo -e "chrII_reverse\n$(cat chrII_reverse.fa )" > chrII_reverse.fa #Add #FirstLine #Text

Multifasta to singleline fasta. $ awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < file.fa #Multi #Single #Fasta #Convert

Split the fasta $ pyfasta split -k 100 -o 20 input.fasta -n 1 #split #pyfasta #overlaps

Nice genome assembly tutorial http://aidenlab.org/assembly/manual_180322.pdf #Assembly #Tutorial #Genome #NGS

Remove empty line from fasta. $ sed -i '/^$/d' standard_output.final.scaffolds_online.fasta #Empty #Fasta #Remove

MultiLine fasta to oneline fasta converter awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < file.fa #Multiline #Oneline

Understanding Paired End and Mate pair reads http://www.biorigami.com/wp-content/uploads/2012/02/PAIREDEND-MATEPAIR.pdf #Reads #Mate #Pairs #PE #Reads #MatePair

http://loupe.10xgenomics.com #10XGenomics #10X #Phase #Haplotype #View

Genome Assembly Cookbook http://aidenlab.org/assembly/manual_180322.pdf #HiC #3D-DNA #Juicer

https://github.com/Ensembl/ensembl-vep #Variant #Effect #Predictor #Github

Variant Effect Predictor http://www.ensembl.org/Tools/VEP #Variant #Effect #Predictor

Efficiency of #PacBio long read #correction by 2nd generation #Illumina sequencing https://www.sciencedirect.com/science/article/pii/S0888754317301660