BOL

#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

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...

#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/

Quality assessment of this mRNA Transcript Assembly Software is described in EvidentialGene_quality. Too many transcript assemblies is much better than too few. It allows one then to apply biological criteria to pick out the best ones. Don't...

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

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