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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

Heatmapper is a freely available web server that allows users to interactively visualize their data in the form of heat maps through an easy-to-use graphical interface. Heatmapper is a versatile tool that allows users to easily create a wide variety...

GRSR is a Tool for Deriving Genome Rearrangement Scenarios for Multiple Uni-chromosomal Genomes. This tool will do the following steps: Step 1. Run mugsy to get multiple sequence alignment results. Step 2 & 3. Extraction of the Coordinates...

MimicrEE2, a multi-threaded Java program for genome-wide forward simulations of evolving populations. MimicrEE2 enables the convenient usage of available genomic resources, supports biological particulars of model organism frequently used in E&R...

You need to run bwa index  $ bwa index genome.fa[bwa_index] Pack FASTA... 1.64 sec[bwa_index] Construct BWT for the packed sequence...[BWTIncCreate] textLength=235383718, availableWord=28562204[BWTIncConstructFromPacked] 10 iterations done....

I receive this error while mapping with BWA MEM ! How to fix it ?

S-plot2 creates an interactive, two-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). In S-plot2, whole eukaryotic chromosomes and smaller prokaryotic genomes can...

HM2 can process any diploid assemblies, but it is especially suitable for diploid assemblies with high heterozygosity (≥3%), which can be difficult for other tools. This pipeline also implements flexible and sensitive assembly error detection, a...

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

rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT)...

In general intereration point of view, the 3C probe for an interaction between two specific regions that you identify a priori. In 4C, one fragment of interest is known, and you probe for all the potential fragments interacting with your...

3C: chromosome conformation capture 4C:chromosome conformation capture-on-chip 5C : chromosome conformation capture carbon copy

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