Once a query gene has been entered, it is displayed in its genomic context in parallel to the genomic context of all its orthologous and paralogous copies in all the other sequenced metazoan genomes. Moreover, Genomicus stores and displays the predicted ancestral genome structure in all the ancestral species within the phylogenetic range of interest.

All the data on extant species displayed in this browser are from Ensembl.

Address of the bookmark: http://genomicus.biologie.ens.fr/genomicus-90.01/cgi-bin/search.pl

Address of the bookmark: https://sourceforge.net/projects/genomeview/

Address of the bookmark: https://github.com/CAFS-bioinformatics/LR_Gapcloser

It demonstrates how to use long PacBio sequencing reads to assemble a bacterial genome, and includes additional steps for circularising, trimming, finding plasmids, and correcting the assembly with short-read Illumina data.

 Please comment if you know any other long read addembly tutorial.

Address of the bookmark: http://sepsis-omics.github.io/tutorials/modules/cmdline_assembly_v2/

In this report, we compare and evaluate several genome assembly software based on TSG technology. The experimentation has been performed on 4 reference genomes and the results evaluated with the QUAST software. The 11 software that have been evaluated are: Celera Assembler , Falcon , Miniasm, Newbler , SGA Assembler, Smartdenovo, Abruijn, Ra, DBG2OLC, Spades and Cerulean. The first 8 software use only long reads, while the 3 last software can merge long and short reads

where, c is the count of a k-mer from reads, m is the mode of counts of read k-mers, and n is the copy of the k-mer in the assembly.

Address of the bookmark: https://github.com/liu3zhenlab/KAD

You can try this here, or try it later on your own data.

Get data

We will use the same Illumina data as we used above:

• illumina_R1.fastq.gz: the Illumina forward reads
• illumina_R2.fastq.gz: the Illumina reverse reads

Assemble

Run Spades:

spades.py -1 illumina_R1.fastq.gz -2 illumina_R2.fastq.gz --careful --cov-cutoff auto -o spades_assembly_all_illumina

• -1 is input file of forward reads
• -2 is input file of reverse reads
• --careful minimizes mismatches and short indels
• --cov-cutoff auto computes the coverage threshold (rather than the default setting, “off”)
• -o is the output directory

Results

Move into the output directory and look at the contigs:

infoseq contigs.fasta

Address of the bookmark: https://ics.hutton.ac.uk/strudel/

Training Resources:

• Bioinformatics Workshop (Webinars)
• Bioinformatics Training Slides

Specialized Applications:

• De Novo Assembly
• Transcriptome analysis
• Base Modification Analysis
• Barcoding
• Data Analysis Tools
• Minor Variants and Phasing Analysis

Address of the bookmark: https://github.com/PacificBiosciences/Bioinformatics-Training/wiki

If you have any questions or comments, post them on one of the trackers on BRIG’s SourceForge page:http://sourceforge.net/tracker/?group_id=328245.

Features:

• Images show similarity between a central reference sequence and other sequences as concentric rings.
• BRIG will perform all BLAST comparisons and file parsing automatically via a simple GUI.
• Contig boundaries and read coverage can be displayed for draft genomes; customized graphs and annotations can be displayed.
• Using a user-defined set of genes as input, BRIG can display gene presence, absence, truncation or sequence variation in a set of complete genomes, draft genomes or even raw, unassembled sequence data.
• BRIG also accepts SAM-formatted read-mapping files enabling genomic regions present in unassembled sequence data from multiple samples to be compared simultaneously

Address of the bookmark: http://brig.sourceforge.net/