BOL: Related items

Common steps for reads mapping !

BioStar — Thu, 09 Mar 2023 02:48:02 -0600

Mapping reads to a reference genome is an essential step in many types of genomic analysis, such as variant calling and gene expression analysis. Here are some general steps to follow for mapping reads to a genome:

Choose a read mapper: There are many read mappers available, such as BWA, Bowtie, and HISAT2. Choose a mapper that is appropriate for your type of data and research question.
Index the reference genome: Before mapping reads, the reference genome needs to be indexed. This involves creating an index of the genome sequence that allows the mapper to quickly find matches to the reads. Most mappers have their own indexing tools.
Prepare the read data: The reads should be in a format that is compatible with the mapper. Most mappers accept FASTQ or BAM files. Depending on the quality of the data, it may need to be filtered or trimmed before mapping.
Run the mapper: The mapper is run with the command-line interface or using a graphical user interface. The specific command depends on the mapper being used, but typically involves specifying the input data, reference genome, and output file format.
Evaluate the mapping results: After the mapping is complete, the results should be evaluated. This includes assessing the quality of the mapping, such as the mapping rate, the number of mapped reads, and the mapping quality score.
Post-processing: Depending on the analysis being performed, post-processing of the mapped reads may be necessary. This can include filtering reads based on quality, removing duplicate reads, and calling variants.

Overall, mapping reads to a reference genome is a complex process that requires careful consideration of the type of data, the research question, and the specific mapper being used.

List of bioinformatics workflow management tools !

Rahul Nayak — Sat, 20 Mar 2021 00:15:25 -0500

Here are list of Workflow Managers

BigDataScript – A cross-system scripting language for working with big data pipelines in computer systems of different sizes and capabilities. [ paper-2014 | web ]
Bpipe – A small language for defining pipeline stages and linking them together to make pipelines. [ web ]
Common Workflow Language – a specification for describing analysis workflows and tools that are portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. [ web ]
Cromwell – A Workflow Management System geared towards scientific workflows. [ web ]
Galaxy – a popular open-source, web-based platform for data intensive biomedical research. Has several features, from data analysis to workflow management to visualization tools. [ paper-2018 | web ]
Nextflow (recommended) – A fluent DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner. [ paper-2018 | web ]
Ruffus – Computation Pipeline library for python widely used in science and bioinformatics. [ paper-2010 | web ]
SeqWare – Hadoop Oozie-based workflow system focused on genomics data analysis in cloud environments. [ paper-2010 | web ]
Snakemake – A workflow management system in Python that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment. [ paper-2018 | web ]
Workflow Descriptor Language – Workflow standard developed by the Broad. [ web ]

Qualimap2: Evaluating next generation sequencing alignment data

Jit — Tue, 11 Sep 2018 04:44:29 -0500

Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.

Supported types of experiments include:

Whole-genome sequencing
Whole-exome sequencing
RNA-seq (speical mode available)
ChIP-seq

Address of the bookmark: http://qualimap.bioinfo.cipf.es/

Pacasus: Correction of palindromes in long reads from PacBio and Nanopore

BioStar — Mon, 12 Nov 2018 05:26:48 -0600

Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification. Check the poster from the Revolutionizing Next-Generation Sequencing (2nd edition) conference in the source folder: https://github.com/swarris/Pacasus/blob/master/vib2017.pdf.

The prepint version is found on http://www.biorxiv.org/content/early/2017/08/09/173872

It uses the pyPaSWAS framework for sequence alignment (https://github.com/swarris/pyPaSWAS)

Address of the bookmark: https://github.com/swarris/Pacasus

Shasta long read assembler

Jit — Tue, 14 Jan 2020 06:47:07 -0600

The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells.

Computational methods used by the Shasta assembler include:

Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in homopolymer repeat counts, which are the most common type of errors in Oxford Nanopore reads.
Using in some phases of the computation a representation of the read sequence based on markers, a fixed subset of short k-mers (k ≈ 10).

More at https://chanzuckerberg.github.io/shasta/index.html

Address of the bookmark: https://github.com/chanzuckerberg/shasta

mutatrix: a population genome simulator which generates simulated genomes.

Jit — Tue, 28 Jan 2020 04:06:58 -0600

genome simulation across a population with zeta-distributed allele frequency, snps, insertions, deletions, and multi-nucleotide polymorphisms

More at https://github.com/ekg/mutatrix

./mutatrix -S sample -P test/ -p 2 -n 10 reference.fasta

Address of the bookmark: https://github.com/ekg/mutatrix

MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (v4) to detect variants.

Rahul Nayak — Wed, 27 Apr 2022 04:34:12 -0500

MUM&Co is able to detect:
Deletions, insertions, tandem duplications and tandem contractions (>=50bp & <=150kb)
Inversions (>=1kb) and translocations (>=10kb)

Address of the bookmark: https://github.com/SAMtoBAM/MUMandCo

Ensembl 77 has been released!

Seema Singh — Sun, 05 Oct 2014 16:38:58 -0500

New updates in e!77 !!

Updated human gene set (GENCODE 21)
Updated rat gene set including manual annotation from HAVANA
New species: Vervet-African green monkey
Imported Transcript Support Levels (TSLs) from UCSC for human and mouse
Imported APPRIS flag for human and mouse
Updated Amazon molly gene set

Find more at http://www.ensembl.info/blog/2014/10/02/ensembl-77-has-been-released/

Structural polymorphism analysis from NGS data

Sat, 13 Jul 2013 17:12:47 -0500

The LabEx BASC (Biodiversity, Agroecosystems, Society, Climate), a network of 13 laboratories of the Paris-Saclay Scientific Cluster, is seeking a bioinformatician to analyze Next Generation Sequencing (NGS) data analysis. In the context of a flagship project aiming at understanding and improving the adaptive capacity of agroecosystems it will be critical to establish a link between sequence variation, functional variation, gene/protein expression and phenotypic adaptation.

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.

Postdoc Positions - Mammalian Transcriptome Evolution at SIB

Mon, 12 Aug 2013 19:58:33 -0500

BIOINFORMATICS POSTDOC IN FUNCTIONAL EVOLUTIONARY GENOMICS

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