BOL: Related items

HapSolo: An optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding

Jit — Sat, 08 May 2021 21:25:00 -0500

HapSolo, that identifies secondary contigs and defines a primary assembly based on multiple pairwise contig alignment metrics. HapSolo evaluates candidate primary assemblies using BUSCO scores and then distinguishes among candidate assemblies using a cost function. The cost function can be defined by the user but by default considers the number of missing, duplicated and single BUSCO genes within the assembly. HapSolo performs hill climbing to minimize cost over thousands of candidate assemblies.

Address of the bookmark: https://github.com/esolares/HapSolo

Bioistats Online course

Abhimanyu Singh — Thu, 10 Nov 2016 04:22:51 -0600

One of our primary focuses will be to develop an understanding of the various ways in which we can assign a probability to some chance event. We'll also learn the fundamental properties of probability, investigate how probability behaves, and learn how to calculate the probability of a new chance event.

This book is handy understanding basic concepts.

Address of the bookmark: https://onlinecourses.science.psu.edu/stat414/node/287

Illumina based assembly pipeline steps !

Surabhi Chaudhary — Fri, 10 Dec 2021 06:22:54 -0600

Illumina

Merge re-sequenced FastQ files (cat)
Read QC (FastQC)
Adapter trimming (fastp)
Removal of host reads (Kraken 2; optional)
Variant calling
1. Read alignment (Bowtie 2)
2. Sort and index alignments (SAMtools)
3. Primer sequence removal (iVar; amplicon data only)
4. Duplicate read marking (picard; optional)
5. Alignment-level QC (picard, SAMtools)
6. Genome-wide and amplicon coverage QC plots (mosdepth)
7. Choice of multiple variant calling and consensus sequence generation routes (iVar variants and consensus; default for amplicon data || BCFTools, BEDTools; default for metagenomics data)
  - Variant annotation (SnpEff, SnpSift)
  - Consensus assessment report (QUAST)
  - Lineage analysis (Pangolin)
  - Clade assignment, mutation calling and sequence quality checks (Nextclade)
  - Individual variant screenshots with annotation tracks (ASCIIGenome)
8. Intersect variants across callers (BCFTools)
De novo assembly
1. Primer trimming (Cutadapt; amplicon data only)
2. Choice of multiple assembly tools (SPAdes || Unicycler || minia)
  - Blast to reference genome (blastn)
  - Contiguate assembly (ABACAS)
  - Assembly report (PlasmidID)
  - Assembly assessment report (QUAST)
Present QC and visualisation for raw read, alignment, assembly and variant calling results (MultiQC)

Research Officer at National Tea Research Foundation

Fri, 18 Nov 2016 04:19:24 -0600

National Tea Research Foundation (NTRF) a registered body, requires qualified and experienced agricultural research scientist for contractual appointment as per details below :

Post Research Officer, NTRF, Kolkata

Essential Post Graduate degree in Life Science having special paper in Bioinformatics. Post Graduate degree in Bioinformatics.

Desirable Ph. D. in the area of computational biology or bioinformatics.

Job Experience Work experience on database development, capable to work independently and efficient in bioinformatics related project.

Job Responsibility

To develop database on various aspects of tea research.

Screening of the In-house projects of NTRF at the preliminary level.

Review and evaluation of In-house projects of NTRF. Technical monitoring of the In-house projects of NTRF.

Reviewing the final technical report of the In-house projects of NTRF.

Putting-up of same proposals for taking approval and sanction of the competent authority.

Physical and technical verification of the In-house projects of NTRF.

To assist in organizing seminars / workshops / meetings etc.

Interested candidate may appear for walk-in Interview on 17 th November, 2016

More Info :

http://www.teaboard.gov.in/pdf/Recruitment_for_the_post_of_Research_Officer_pdf7538.pdf

Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation

Neel — Sun, 03 Apr 2022 20:35:19 -0500

Merfin, a k-mer based variant-filtering algorithm for improved accuracy in genotyping and genome assembly polishing. Merfin evaluates each variant based on the expected k-mer multiplicity in the reads, independently of the quality of the read alignment and variant caller’s internal score. Merfin increased the precision of genotyped calls in several benchmarks, improved consensus accuracy and reduced frameshift errors when applied to human and nonhuman assemblies built from Pacific Biosciences HiFi and continuous long reads or Oxford Nanopore reads, including the first complete human genome. Moreover, we introduce assembly quality and completeness metrics that account for the expected genomic copy numbers.

More at https://www.nature.com/articles/s41592-022-01445-y

Address of the bookmark: https://github.com/arangrhie/merfin

Spines

Jit — Mon, 28 Nov 2016 05:33:26 -0600

Spines is a collection of software tools, developed and used by the Vertebrate Genome Biology Group at the Broad Institute. It provides basic data structures for efficient data manipulation (mostly genomic sequences, alignments, variation etc.), as well as specialized tool sets for various analyses. It also features three sequence alignment packages: Satsuma, a highly parallelized program for high-sensitivity, genome-wide synteny; Papaya, an all-purpose alignment tool for less diverged sequences; and SLAP, a context-sensitive local aligner for diverged sequences with large gaps.

Access Spines here.

Address of the bookmark: https://www.broadinstitute.org/genome-sequencing-and-analysis/spines

MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads

Abhi — Tue, 05 Sep 2023 07:31:35 -0500

MitoHiFi v3.2 is a python pipeline distributed under MIT License !

MitoHiFi was first developed to assemble the mitogenomes for a wide range of species in the Darwin Tree of Life Project (DToL)

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05385-y

Address of the bookmark: https://github.com/marcelauliano/MitoHiFi

bipype

Jit — Thu, 01 Dec 2016 08:47:38 -0600

Bipype is a very useful program, which prepare a lot of types of bioinformatics analyses. There are three input options: amplicons, WGS (whole genome sequences) and metatranscriptomic data. If amplicons are input data, then bipype does reconstruction and pairs merging. After that biodiversity is searching. There are two types of searching depending on the amplicons types (ITS or 16S). If WGS are chosen, then bipype finds the SA coordinates of the input reads and generates alignments in the SAM format given single-end reads, aligns reads to reference sequence(s). All of these analyses will be shown with Krona program, which allows to show hierarchical data with pie charts.

Address of the bookmark: https://readthedocs.org/projects/bipype/

TRITEX, a computational pipeline for chromosome-scale assembly of plant genomes

LEGE — Fri, 14 Feb 2025 10:53:48 -0600

This is the documentation of TRITEX, a computational pipeline for chromosome-scale assembly of plant genomes. It was developed in the research group Domestication Genomics at the Leibniz Institute of Plant Genetics and Crop Research (IPK) Gatersleben.

Address of the bookmark: https://tritexassembly.bitbucket.io/

16th Congress of the European Society for Evolutionary Biology (ESEB)

Thu, 22 Dec 2016 08:08:37 -0600

Abstract submissions for our upcoming symposium on the Genomics of Adaptation that will take place as part of the 16th Congress of the European Society for Evolutionary Biology (ESEB). The conference will take place from August 20th - August 25th, 2017 in Groningen, the Netherlands.

SYMPOSIUM DESCRIPTION: Genomics of Adaptation [S16] Model organisms for life-history research are mainly studied in the lab where functional genetics is assessable. In general, however, knowledge about their eco-evolutionary dynamics, such as biotic interactions, is rare. By contrast, in organisms for which the ecology and adaptation strategies in the field are well known, we typically lack the appropriate genetic tools to investigate functionality. Advances in genomics and statistics as well as investments in evolutionary model organisms are now providing access to putatively adaptive genome-wide variation within species from across the tree of life. In this symposium, we focus on integrating life-history biology, genetics and evolutionary ecology in the genomics era.

We wish to (1) highlight the role of genetic architecture of complex traits, such as adaptations to biotic interactions or life-history traits; (2) contrast this to morphological traits which are generally thought to have a less complex genetic architecture; and (3) discuss the opportunities and drawbacks of specific model systems.

INVITED SPEAKERS: Josephine Pemberton, University of Cambridge (http://bit.ly/2hJWytJ ) Peter Tiffin, University of Minnesota (http://bit.ly/2hK7HuS )

ABSTRACT SUBMISSION The deadline for abstract submission is January 10, 2017. For more information and to submit abstracts online, please visit: http://bit.ly/2fBXlvN We look forward to an exciting symposium and seeing you all in Groningen! Sincerely, Ben Blackman, UC Berkeley Maaike de Jong, University of Bristol Bart Pannebakker, Wageningen University Noah Whiteman, UC Berkeley Jelle Zandveld, Wageningen University