BOL: Related items

DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication

Jit — Tue, 14 Nov 2017 10:26:16 -0600

We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7,000 jobs have been processed since its first launch in 2016. Here, we present a newly implemented background annotation engine for DFAST, which is also available as a standalone command-line program. The new engine can annotate a typical-sized bacterial genome within 10 minutes, with rich information such as pseudogenes, translation exceptions, and orthologous gene assignment between given reference genomes. In addition, the modular framework of DFAST allows users to customize the annotation workflow easily and will also facilitate extensions for new functions and incorporation of new tools in the future.

Availability and Implementation

The software is implemented in Python 3 and runs in both Python 2.7 and 3.4– on Macintosh and Linux systems. It is freely available at https://github.com/nigyta/dfast_core/ under the GPLv3 license with external binaries bundled in the software distribution. An on-line version is also available at https://dfast.nig.ac.jp/.

Address of the bookmark: https://dfast.nig.ac.jp/

CANU genome assembly parameters !

Rahul Nayak — Mon, 07 Jan 2019 08:40:37 -0600

Choose the appropriate parameters to run Canu and run it. The assembly will take about an hour. You can use two cores (parameter -maxThreads=2) and you would like to disable cluster option, since we compute on a single Amazon server set off the option to compute on cluster useGrid=false. This specifications should be for your project discussed with a local computing guru. The parameters that are in square brackets [] are optional, symbol | stands for "or".

usage:   canu [-correct | -trim | -assemble | -trim-assemble] \
              [-s ] \
               -p  \
               -d  \
               genomeSize=[g|m|k] \
               -maxThreads=2 \
               useGrid=false \
              [other-options] \
               read_file.fastq.gz

A default Canu run produces usually high quality assembly, example of a command that was used for testing can be found below. However, there are still a lot of parameters that are possible to tweak. For example if we desire to assemble haplotypes separately of if we want to smash them together, we can alternate the error correction process.

canu -p test_asmbl \
     -d asm_test3 \
     genomeSize=2m \
     -maxThreads=2 useGrid=false \
     -pacbio-raw \ ~/pacbio/dna/sample_reads.fastq.gz

There is a brilliant section in documentation about parameter tweaking.

The output directory contains will contain many files. The most interesting ones are:

*.correctedReads.fasta.gz : file containing the input sequences after correction, trim and split based on consensus evidence.
*.trimmedReads.fastq : file containing the sequences after correction and final trimming
*.layout : file containing informations about read inclusion in the final assembly
*.gfa : file containing the assembly graph by Canu
*.contigs.fasta : file containing everything that could be assembled and is part of the primary assembly

The basic stats of assembly can be read from reports generated by the assembler, or calculated using standard UNIX command line tools.

More at https://canu.readthedocs.io/en/latest/faq.html

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

Biological databases !

BioStar — Wed, 12 Feb 2020 01:16:29 -0600

Now a days there are a lots of genomics databases available around the world. This bookmark is created to provide all links in one place ...

ftp://ftp.ncbi.nih.gov/genomes/

https://hgdownload.soe.ucsc.edu/downloads.html

Address of the bookmark: ftp://ftp.ncbi.nih.gov/genomes/

Understanding kmer !

BioStar — Wed, 18 Aug 2021 04:27:51 -0500

What is a k-mer anyway? A k-mer is just a sequence of k characters in a string (or nucleotides in a DNA sequence). Now, it is important to remember that to get all k-mers from a sequence you need to get the first k characters, then move just a single character for the start of the next k-mer and so on. Effectively, this will create sequences that overlap in k-1 positions.

Address of the bookmark: https://bioinfologics.github.io/post/2018/09/17/k-mer-counting-part-i-introduction/

quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification.

Abhi — Sat, 08 Jun 2024 15:54:36 -0500

quarTeT is a collection of tools for T2T genome assembly and basic analysis in automatic workflow.

Task include:

AssemblyMapper : reference-guided genome assembly
GapFiller : long-reads based gap filling
TeloExplorer : telomere identification
CentroMiner : centromere candidate prediction

https://academic.oup.com/hr/article/10/8/uhad127/7197191?login=false

Address of the bookmark: http://www.atcgn.com:8080/quarTeT/home.html

Katju Lab

Fri, 26 Feb 2016 03:25:32 -0600

TheLab seek to understand the genetic factors contributing to genomic variation and phenotypic diversity. To this end, we employ molecular and bioinformatic tools to study evolutionary processes at the level of populations, both experimental and natural, and genomes. Our research interests encompass a wide range of topics, including the evolution of organellar and nuclear genomes, gene duplication and the origin of novel function, and the fitness and phenotypic consequences of mutation in evolution. For details regards ongoing projects, please see the Research page.

http://katjulab.com/research.html

BUSCO

Jitendra Narayan — Sun, 07 Feb 2016 16:02:39 -0600

Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs

More at http://busco.ezlab.org/

Address of the bookmark: http://busco.ezlab.org/

RCircos: an R package for Circos 2D track plots

Jit — Fri, 20 May 2016 11:01:13 -0500

RCircos package provides a simple and flexible way to make Circos 2D track plots with R and could be easily integrated into other R data processing and graphic manipulation pipelines for presenting large-scale multi-sample genomic research data. It can also serve as a base tool to generate complex Circos images.

More at https://bitbucket.org/henryhzhang/rcircos/src

Address of the bookmark: https://bitbucket.org/henryhzhang/rcircos/src

Understanding Greedy Algorithms

Jit — Mon, 12 Dec 2016 04:37:40 -0600

Learning greedy algo for biologist.

https://www.topcoder.com/community/data-science/data-science-tutorials/greedy-is-good/

This webpage is also useful for the same:

http://learninglover.com/examples.php?id=59

http://www.cs.rpi.edu/~magdon/ps/conference/super_biokdd.pdf

https://ocw.mit.edu/courses/biology/7-91j-foundations-of-computational-and-systems-biology-spring-2014/lecture-slides/MIT7_91JS14_Lecture6.pdf

http://schatzlab.cshl.edu/teaching/AssemblyClass/01.%20Assembly%20Intro.pdf

http://lsl.sinica.edu.tw/Services/Class/files/20150612449.pdf

http://www.cs.jhu.edu/~langmea/resources/lecture_notes/assembly_scs.pdf

https://www2.eecs.berkeley.edu/Pubs/TechRpts/2016/EECS-2016-43.pdf

Address of the bookmark: https://www.topcoder.com/community/data-science/data-science-tutorials/greedy-is-good/