BOL

Phased the genome http://pb-falcon.readthedocs.io/en/latest/_downloads/Kingan_DiploidGenome_ECUGM2017_BFX.pdf #Falcon #Unzip #PPT

Download and install MUMmer Align your assembly to a reference genome using nucmer (from MUMmer package) $ nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT Consult the MUMmer manual if you encounter problems Optional: Gzip...

#Convert a #multi-line #fasta to a #singleline #fasta $ awk '!/^>/ { printf "%s", $0; n = "\n" } /^>/ { print n $0; n = "" } END { printf "%s", n }' sample1.fa > sample1_singleline.fa

RestrictionDigest can simulate the reference genome digestion and generate comprehensive information of the simulation. It can simulate single-enzyme digestion, double-enzyme digestion and size selection process. It can also analyze multiple genomes...

sed -i -e '/^+/,/^\@/{/^+/!{/^\@/!d}}; /^+/ d; s/@/>/g' OUTPUT.fastq > out.fa #Convert

Please visit this https://bioinformaticsonline.com/search?q=ont&entity_type=object&entity_subtype=bookmarks&offset=0&search_type=entities

Breakpointer is a fast tool for locating sequence breakpoints from the alignment of single end reads (SE) produced by next generation sequencing (NGS). It adopts a heuristic method in searching for local mapping signatures created by...

P_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs,...

HiGlass is a tool for exploring genomic contact matrices and tracks. Please take a look at the examples and documentation for a description of the ways that it can be configured to explore and compare contact matrices. To load private data, HiGlass...

D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation. We use minimap...

Finding coding regions in DNA sequences http://genome.crg.es/courses/Lisbon04/exercises/day2/Perl_programming/index.html #Perl #Genes #Script

GMcloser uses likelihood-based classifiers calculated from the alignment statistics between scaffolds, contigs and paired-end reads to correctly assign contigs or long reads to gap regions of scaffolds, thereby achieving accurate and efficient gap...

npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be integrated with simple...

The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide databases in an attempt to obtain all sequences that...