Address of the bookmark: https://github.com/Megagenomics/FastProNGS

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

1. Co-assembly procedure with read mapping for estimation of the abundances of genes in each metagenome
2. Co-assembly of a large number of metagenomes via merging of individual metagenomes
3. Includes binning and bin checking, for retrieving individual genomes
4. The results are stored in a database, where they can be easily exported and shared, and can be inspected anywhere using a web interface.
5. Internal checks for the assembly and binning steps inform about the consistency of contigs and bins, allowing to spot potential chimeras.
6. Metatranscriptomic support via mapping of cDNA reads against reference metagenomes

Address of the bookmark: https://github.com/jtamames/SqueezeMeta

Using the reference sequence dictionary (*.dict), it also creates some empty BAM files if no sam record was found for a chromosome. A pair of 'mock' SAM-Records can also be added to those empty BAMs to avoid some tools (like samtools) to crash.

Usage

java -jar splitbam.jar -p OUT/__CHROM__/__CHROM__.bam -R ref.fasta (bam|sam|stdin)

Options

• -h help; This screen.
• -R (indexed reference file) REQUIRED.
• -u (unmapped chromosome name): default:Unmapped
• -e | --empty : generate EMPTY bams for chromosome having no read mapped
• -m | --mock : if option '-e', add a mock pair of sam records to the empty bam
• -p (output file/bam pattern) REQUIRED. MUST contain __CHROM__ and end with .bam
• -s assume input is sorted.
• -x | --index create index.
• -t | --tmp (dir) tmp file directory
• -G (file) chrom-group file (see below)

Address of the bookmark: https://code.google.com/archive/p/jvarkit/wikis/SplitBam.wiki

QuorUM is distributed as an independent software package and as a module of the MaSuRCA assembly software. Both are available under the GPL open source license at http://www.genome.umd.edu.

Address of the bookmark: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130821

https://nxrepair.readthedocs.io/en/latest/tutorial.html

nxrepair aligned_matepairs.bam assemblyfasta.fasta error_locations.csv new_fasta.fasta

Address of the bookmark: https://github.com/rebeccaroisin/nxrepair

BEAR is intended to be an easy-to-use collection of scripts for generating simulated WGS metagenomic reads with read lengths, quality scores, error profiles, and species abundances derived from real user-supplied WGS data.

Address of the bookmark: https://github.com/sej917/BEAR

The consequences of AMR are profound and multifaceted. Medically, it leads to treatment failures, prolonged illnesses, and increased mortality rates, as common infections become more challenging to manage. The economic burden of AMR is substantial, as it escalates healthcare costs due to longer hospital stays, the need for more potent and expensive drugs, and the potential loss of productivity in affected individuals. Furthermore, AMR jeopardizes global health security, as the emergence of multidrug-resistant pathogens makes it increasingly difficult to respond to infectious disease outbreaks and bioterrorism threats.

To address AMR, a multidisciplinary approach is essential. This includes improved antimicrobial stewardship practices in healthcare settings, raising public awareness about the responsible use of antibiotics, and developing rapid diagnostic tests to guide precise treatment decisions. Additionally, there is a crucial need for continued research into the development of novel antimicrobial agents and vaccines. Collaborative efforts among scientists, clinicians, policymakers, and the pharmaceutical industry are essential to mitigate the impact of AMR and ensure that our arsenal of effective treatments remains robust in the face of evolving microbial threats. In the absence of concerted global action, the specter of untreatable infections looms, underscoring the urgency of addressing AMR as a critical public health priority.

The successful candidate will be in charge of the detection of polymorphisms including structural variants, of the comparison of multiple and diverse genomes of a same species and of the construction of pan- and core-genomes. These challenging tasks will require bioinformatics developments and implementation of methods for accommodating the high level of repetitiveness of complex genomes. The tools will be integrated into pipelines and made available to end-users through the Galaxy platform. The bioinformatician will therefore also have to provide researchers with advices on their experimental designs in order to ensure compliance of produced datasets with pipelines requirements. He/she will be hosted by a bioinformatics/informatics team (7 people) (http://moulon.inra.fr/index.php/fr/equipestransversales/atelier-de-bioinformatique) which has computational facilities and expertise in NGS data analysis, and will benefit as well from national and international collaborative networks (Aplibio http://www.renabi.fr/platforms/aplibio/, Transplant http://transplantdb.eu, AMAIZING http://www.amaizing.fr/).

The position requires a doctoral degree (PhD) in bioinformatics with strong expertise in script writing (Python/Perl) and pipeline development.

Applicants should send a CV and the names of 2 referees willing to provide a letter of recommendation to joets@moulon.inra.fr.

Center for Integrative Genomics, University of Lausanne, Switzerland

Two postdoctoral positions (2 years with possible extensions up to 5 years) are available immediately in the evolutionary genomics group of Henrik Kaessmann.

We are seeking highly qualified and enthusiastic applicants with strong skills in computational biology/bioinformatics, preferably also with experience in data mining and comparative or evolutionary genome analysis.

We have been interested in a range of topics related to the functional evolution of genomes from primates (e.g., the emergence of new genes and their functions) and other mammals (e.g., the origin and evolution of mammalian sex chromosomes). In the framework of a recently launched series of projects, a large amount of transcriptome and genome (e.g., epigenome) data are being produced by the wet lab unit of the group using next generation sequencing technologies for a unique collection of tissues from representative mammals and outgroup species (e.g., birds). Topics of current projects based on these data include the origins and/or evolution of protein-coding genes, alternative splicing, microRNAs, long noncoding RNAs, and dosage compensation.

The postdoctoral fellow will perform integrated evolutionary/bioinformatics analyses based on data produced in the lab and available genomic data. The specific project will be developed together with the candidate.

The language of the institute is English, and its members form an international group that is rapidly expanding. The institute is located in Lausanne, a beautiful city at Lake Geneva.

For more information on the group and our institute more generally, please refer to our website: http://www.unil.ch/cig/page7858_en.html

Please submit a CV, statement of research interest, and names of three references to: Henrik Kaessmann (Henrik.Kaessmann@unil.ch).

Webpage : http://www.unil.ch/cig/page7858.html