BOL

ALLHiC: identify allelic contigs https://github.com/tangerzhang/ALLHiC/wiki/ALLHiC:-identify-allelic-contigs #AllHic #Scaffolding #3C #ALLHiC

De novo genome assembly https://astrobiomike.github.io/genomics/de_novo_assembly #Genome #Assembly #DeNovo #Genome

Errors in sequence assembly and corrections (Bioinformatics) http://what-when-how.com/bioinformatics/errors-in-sequence-assembly-and-corrections-bioinformatics/ #Assembly #Error

Long read assembly workshop https://www.melbournebioinformatics.org.au/tutorials/tutorials/pacbio/ #Long #Reads #Assembly #PacBio #Learn #Tutorial #Workshop

https://bioinformaticsdotca.github.io/high-throughput_biology_2017 #NGS #Tutorial #Learn #Assembly

Fastq 2 fasta convert $ sed '/^@/!d;s//>/;N' sample1.fq > sample1.fa #fastq2fasta #fastqtwofasta

One liner to remove the description information from a fasta file and just keep the identifier $ perl -p -i -e 's/>(.+?) .+/>$1/g' sample1.fa #clean #header #fasta

This script will #extract the intron feature #gff3 and sequence from gene_exon gff3 and fasta file. Extract-intron-from-gff3

A De Novo Genome #Assembly Algorithm for #Repeats and Nonrepeats https://www.hindawi.com/journals/bmri/2014/736473/

The #p53 #pathway: positive and negative feedback loops https://www.nature.com/articles/1208615

ATM, ATR, and DNA-PK: The Trinity at the Heart of the #DNA #Damage Response https://www.sciencedirect.com/science/article/pii/S1097276517303544

Split a multi-FASTA file into individual FASTA files: awk '/^>/{s=++d".fa"} {print > s}' multi.fa #split #multifasta

Merge overlapping bed file https://bedtools.readthedocs.io/en/latest/content/tools/merge.html #bed #merge #overlapping

make a window of 60k of bed file. $ bedtools makewindows -g genome -w 60000 > 60K.windows.bed #bed #bin #window

Long reads assembly tutorial https://www.melbournebioinformatics.org.au/tutorials/tutorials/pacbio/ #Long #Reads #PacBio #assembly #Genome