BOL: Related items

FERMI

Jit — Fri, 09 Sep 2016 05:37:13 -0500

Fermi is a de novo assembler with a particular focus on assembling Illumina short sequence reads from a mammal-sized genome. In addition to the role of a typical assembler, fermi also aims to preserve heterozygotes which are often collapsed by other assemblers. Its ultimate goal is to find a minimal set of
unitigs to represent all the information in raw reads.

Fermi follows the overlap-layout-consensus paradigm and uses the FM-DNA-index (FMD-index) as the key data structure. It is inspired by the string graph assembler (Simpson and Durbin, 2010 and 2012) and has a similar workflow.

As a typical de novo assembler, fermi tends to produce contigs with slightly longer N50. However, the major weakness of fermi is the high misassembly rate. Although fermi provides a tool to fix misassemblies by using paired-end reads to achieve an accuracy comparable to other assemblers, this is not a favorable solution.

Fermi is designed to be used on a multi-core Linux machine with large shared memory. The easiest way to run fermi is to use the run-fermi.pl script. It generates a Makefile. The actual assembly is done by invoking make. Premature assembly processes can be resumed. Here is an example:

run-fermi.pl -dAPe ./fermi -p NA12878 -t16 -f18 reads*.fq.gz > NA12878.mak
make -f NA12878.mak -j16

Address of the bookmark: https://github.com/lh3/fermi

Converting a VCF into a FASTA given some reference !

Jit — Fri, 20 Jul 2018 10:03:53 -0500

Samtools/BCFtools (Heng Li) provides a Perl script vcfutils.pl which does this, the function vcf2fq (lines 469-528)

This script has been modified by others to convert InDels as well, e.g. this by David Eccles

./vcf2fq.pl -f <input.fasta> <all-site.vcf> > <output.fastq>

https://github.com/gringer/bioinfscripts/blob/master/vcf2fq.pl

https://github.com/lh3/samtools/blob/master/bcftools/vcfutils.pl

SRF Bioinformatics at Bose Institute, India

Thu, 29 Sep 2016 09:39:13 -0500

Advt. No. S/DPB(CB)/17/2016-17
Junior Research Assistant/ Senior Research Assistant Job vacancies in Bose Institute on temporary basis
Project Title : “Genome wide transcriptome analysis to identity MYMIV-stress related genomic resources of blackgram”
Junior Research Assistant
Qualification : Good academic record in B.Sc. and M.Sc. in Botany or Biotechnology from reputed Universities. Must have good practical hand, this should be certified by two Senior/reputed PG teachers on a scale of 10.
Desirable : Preference will be given to those who already have some research experience (for at least 2 months).
Consolidated Pay : Rs. 16,400/- p.m.
Age Limit : Below 28 years (relaxable in case of SC/ST/OBC/Women candidates only as per rules).
Senior Research Assistant
Qualification : B.Sc. in Biotechnology and M.Sc. in Biotechnology or Bioinformatics. Hands on training in Bioinformatics. At least two Research Publications with Bioinformatics components.
Desirable : Preference will be given to the candidates who have previous experience in Next Gen Sequencing data analysis of genomic/transcriptome/miRNA.
Consolidated Pay : Rs. 18,700/- p.m.
Age Limit : Below 30 years (relaxable in case of SC/ST/OBC/Women candidates only as per rules).

http://www.boseinst.ernet.in/advertisement.html

Long read assembly workshop !

Rahul Nayak — Thu, 04 Oct 2018 17:23:18 -0500

This is a tutorial for a workshop on long-read (PacBio) genome assembly.

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/

Murasaki

Anjana — Fri, 30 Sep 2016 10:22:30 -0500

Murasaki is an anchor alignment program that is

exteremely fast (17 CPU hours for whole Human x Mouse genome (with 40 nodes: 35 wall minutes), or 8 mammals in 21 CPU hours (42 wall minutes))
scalable (Arbitrarily parallelizable across multiple nodes using MPI)
memory efficient. (Even a single node with 16GB of ram can handle over 1Gbp of sequence)
unlimited by pattern length or selection
repeat tolerant

Address of the bookmark: http://murasaki.dna.bio.keio.ac.jp/wiki/index.php?Murasaki

SKESA: strategic k-mer extension for scrupulous assemblies

Jit — Wed, 14 Nov 2018 04:45:41 -0600

SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit shows that SKESA produces assemblies that have high sequence quality and contiguity, handles low-level contamination in reads, is fast, and produces an identical assembly for the same input when assembled multiple times with the same or different compute resources.

Source code for SKESA is freely available at https://github.com/ncbi/SKESA/releases.

Research Paper @ Link

SKESA algorithm are as follows:

Address of the bookmark: https://github.com/ncbi/SKESA/releases

MIRO : miRNA omics

Jit — Tue, 04 Oct 2016 14:50:48 -0500

The MIRO (the miRNA omics) pipeline is a flexible and powerful tool for the analysis of miRNA (or more generall short RNA) expression using short-read deep sequencing data. In its present implementation MIRO is especially adapted for the analysis of reads generated with the Illumina sequencing platform. MIRO allows to preprocess the Solexa-reads, map them flexibly to several reference genomes using one of four different mappers, create differential gene (miRNA) expression profiles and cluster reads using one of several algorithm. MIRO output is furthermore compatible with software such as genome browsers and miRDeep.

Address of the bookmark: http://seq.crg.es/download/software/Miro/

Versatile genome assembly evaluation with QUAST-LG

Jit — Fri, 21 Dec 2018 22:06:31 -0600

QUAST-LG is an extension of QUAST intended for evaluating large-scale genome assemblies (up to mammalian-size).

QUAST-LG is included in the QUAST package starting from version 5.0.0 (download the latest release). Run QUAST as usual and do not forget to add ‐‐large option to your command!

A short list of the new features (see CHANGES for all):

Significant speedup achieved by both use of new fast aligner (minimap2) and the refactoring of alignment analyzing modules
New k-mer-based completeness and correctness metrics
BUSCO added for enhanced reference-free analysis
The concept of upper bound assembly (theoretical limits on the assembly completeness and contiguity for a given genome and set of reads)

Address of the bookmark: http://cab.spbu.ru/software/quast-lg/

Entrez Direct: E-utilities on the UNIX Command Line

Anjana — Wed, 19 Oct 2016 08:06:24 -0500

Entrez Direct (EDirect) is an advanced method for accessing the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.

EDirect also provides an argument-driven function that simplifies the extraction of data from document summaries or other results that are returned in structured XML format. This can eliminate the need for writing custom software to answer ad hoc questions. Queries can move seamlessly between EDirect commands and UNIX utilities or scripts to perform actions that cannot be accomplished entirely within Entrez.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/books/NBK179288/

List of tools frequently used while genome assembly

BioStar — Tue, 22 Jan 2019 09:39:02 -0600

List of tools frequently used while genome assembly:

I have used the following assemblers

Spades (v. 3.10.1)
CANU (v. 1.6)
Unicycler (v. v0.4.1)
Miniasm (v. 0.2-r137-dirty)

I have used the following mappers

minimap2 (v. 2.0rc1-r232)
minimap (v. 0.2-r124-dirty)
bwa (v. 0.7.12-r1039)

I have used the following polishing tools

Racon (v. not available)
Pilon (v. 1.18)
Nanopolish (v. 0.8.3)

I have used the following tools to assess genome assembly characteristics

ANI.pl (https://github.com/chjp/ANI)
CheckM (v. 1.0.7)
Prokka (v. 1.12)
QUAST (v. 2.3)
mummer (v. not available)

If you have any ideas or superior tools we have missed please let us know in the comments.