BOL: Related items

splitbam: splits a BAM by chromosomes

Jit — Tue, 28 Feb 2017 09:01:28 -0600

splitbam splits a BAM by chromosomes.

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

Mapping NGS

Abhimanyu Singh — Tue, 02 May 2017 07:58:07 -0500

NGS data are just a bunch of sequences, you have no idea which region in the genome each sequences comes from, which gene it represents...
To know that you have to align the sequences to the reference sequence. The reference sequence is in most cases the full genome sequence but sometimes, a library of EST sequences is used.
In either way, aligning your sequence reads to the reference sequence is called mapping.

The most used mappers of DNA-seq data are BWA and Bowtie for DNA-Seq data and Tophat, STAR or HISAT for RNA-Seq data. Mappers differ in which options they can take in, how fast and how accurate they are. Bowtie is faster than BWA, but looses some sensitivity (does not map an equal amount of reads to the correct position in the genome).

Address of the bookmark: http://wiki.bits.vib.be/index.php/Mapping_of_NGS_data

Prokka: tool for the rapid annotation of prokaryotic genomes

Jit — Mon, 06 Mar 2017 03:49:57 -0600

Prokka is a software tool for the rapid annotation of prokaryotic genomes. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA.

Address of the bookmark: http://www.vicbioinformatics.com/software.prokka.shtml

COCACOLA (binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and paired-end read LinkAge)

Jit — Tue, 07 Mar 2017 08:50:57 -0600

COCACOLA is a general framework that combines different types of information: sequence COmposition, CoverAge across multiple samples, CO-alignment to reference genomes and paired-end reads LinkAge to automatically bin contigs into OTUs. Furthermore, COCACOLA seamlessly embraces customized prior knowledge to facilitate binning accuracy.

News: Python version of COCACOLA is available now!

Address of the bookmark: https://github.com/younglululu/COCACOLA

CABOG: Celera Assembler with Best Overlap Graph

Abhimanyu Singh — Mon, 15 May 2017 05:04:39 -0500

CABOG (Celera Assembler with Best Overlap Graph) is scientific software for DNA research. CABOG has been a critical component of many genome sequencing projects. CABOG operates on small genomes such as bacterial as well as large genomes such as mammalian. CABOG is an extension of the Celera Assembler software that was originally developed at Celera for the 2001 publication of the first draft human genome sequence. The software was released to the public domain in 2004. Its open source repository on Source Forge is an internet resource for scientists around the world.

CABOG is one of many software programs called genome assemblers. These programs exist to overcome the fundamental limitation of all sequencing machines, namely, that they read out very few DNA letters at a time. These programs reconstruct genomes that are billions of letters long from the hundreds of letters per read that modern sequencers provide. What these programs do is often described as a scaled up version of a family solving a jigsaw puzzle.

The CABOG software was the first to accomplish many scientific goals. It was the first to assemble the genome of a multicellular organism (Drosophila melanogaster, 2000). It was the first to assemble both parental haplotypes of one human genome (J. Craig Venter, 2007). It was the first to assemble environmental sequence from the oceans (Sargasso Sea in 2004 and Global Ocean Sampling in 2007). It was first to combine reads from first-generation Sanger sequencing machines and second-generation pyrosequencing machines (Marine microbes, 2006). Today, CABOG is one of the leading assembly programs for data sets that include paired end data from the Roche 454 line of sequencing machines.

Address of the bookmark: http://www.jcvi.org/cms/research/projects/cabog/overview/

Multigenome assembly

Jit — Tue, 14 Mar 2017 04:41:23 -0500

This project contains scripts and tutorials on how to assemble individual microbial genomes from metagenomes, as described in:

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

Mads Albertsen, Philip Hugenholtz, Adam Skarshewski, Gene W. Tyson, Kåre L. Nielsen and Per .H. Nielsen

Nature Biotechnology 2013, doi: 10.1038/nbt.2579

See the associated online guide for detailed information.

https://github.com/MadsAlbertsen/multi-metagenome

Address of the bookmark: https://github.com/MadsAlbertsen/multi-metagenome

Enrichr: a comprehensive gene set enrichment analysis

Jit — Thu, 27 Apr 2017 05:42:09 -0500

Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at: http://amp.pharm.mssm.edu/Enrichr.

https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw377

Address of the bookmark: http://amp.pharm.mssm.edu/Enrichr/

Download assemblies from NCBI

Bulbul — Mon, 15 May 2017 06:02:32 -0500

A new “Download assemblies” button is now available in the Assembly database. This makes it easy to download data for multiple genomes without having to write scripts.

For example, you can run a search in Assembly and use check boxes (see left side of screenshot below) to refine the set of genome assemblies of interest. Then, just open the “Download assemblies” menu, choose the source database (GenBank or RefSeq), choose the file type, and start the download. An archive file will be saved to your computer that can be expanded into a folder containing your selected genome data files.

More at https://ncbiinsights.ncbi.nlm.nih.gov/2017/05/08/genome-data-download-made-easy/

RNA-seq Analysis Workshop Course Materials

Jit — Tue, 03 Jul 2018 08:14:14 -0500

RNAseq can be roughly divided into two "types": Reference genome-based - an assembled genome exists for a species for which an RNAseq experiment is performed. It allows reads to be aligned against the reference genome and significantly improves our ability to reconstruct transcripts. This category would obviously include humans and most model organisms but excludes the majority of truly biologically intereting species (e.g., Hyacinth macaw); Reference genome-free - no genome assembly for the species of interest is available. In this case one would need to assemble the reads into transcripts using de novo approaches. This type of RNAseq is as much of an art as well as science because assembly is heavily parameter-dependent and difficult to do well. In this lesson we will focus on the Reference genome-based type of RNA seq. http://chagall.med.cornell.edu/RNASEQcourse/

Address of the bookmark: http://chagall.med.cornell.edu/RNASEQcourse/

Some useful Bioinformatics links

Jit — Fri, 16 Mar 2018 20:50:10 -0500

Reference-free prediction of rearrangement breakpoint reads | Bioinformatics | Oxford Academic

https://academic.oup.com/bioinformatics/article/30/18/2559/2475628
Reference-free SNP detection: dealing with the data deluge

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4083407/
GATB/DiscoSnp: DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, from raw set(s) of reads.

https://github.com/GATB/DiscoSnp
De novo assembly | Oxford Nanopore Technologies

https://nanoporetech.com/taxonomy/term/131
De novo long-read assembly of a complex animal genome | bioRxiv

https://www.biorxiv.org/content/early/2017/09/10/187054
Rapid de novo assembly of the European eel genome from nanopore sequencing reads | Scientific Reports

https://www.nature.com/articles/s41598-017-07650-6.epdf?author_access_token=dktG7e98wyRJnaEEMTcPqtRgN0jAjWel9jnR3ZoTv0P7E7t-wVGo30iojNO7dICajNY_7PE5xVPv6OoLe7hn9TeUjcZ5umREOzNoPMWkfYH58RS6uxm3vm4e4BG2AA_WKW84i6egKK271NwMq-NfzA%3D%3D
nanoporetech/ont-assembly-polish: ONT assembly and Illumina polishing pipeline

https://github.com/nanoporetech/ont-assembly-polish
Generade-nl/TULIP: TULIP - The Uncorrected Long read Itegration Pipeline

https://github.com/Generade-nl/TULIP
www.nature.com

https://www.nature.com/articles/s41598-017-03996-z
Example gallery of NanoPlot – Gigabase or gigabyte

https://gigabaseorgigabyte.wordpress.com/2017/06/01/example-gallery-of-nanoplot/
Tool documentation

https://broadinstitute.github.io/picard/command-line-overview.html
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. - PubMed - NCBI

https://www.ncbi.nlm.nih.gov/pubmed/24185095
MAFFT ver.7 - a multiple sequence alignment program

https://mafft.cbrc.jp/alignment/software/algorithms/algorithms.html
Measuring the distance between multiple sequence alignments | Bioinformatics | Oxford Academic

https://academic.oup.com/bioinformatics/article/28/4/495/212883
The MUMmer 3 examples

http://mummer.sourceforge.net/examples/
MAFFT ver.7 - a multiple sequence alignment program

https://mafft.cbrc.jp/alignment/software/tips.html
Omega | Overlap-graph de novo Assembler for Metagenomics

https://omega.omicsbio.org/
abiswas-odu/Disco: Multi-threaded Distributed Memory Overlap-Layout-Consensus (OLC) Metagenome Assembler

https://github.com/abiswas-odu/Disco
SAGE: String-overlap Assembly of GEnomes | BMC Bioinformatics | Full Text

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-302

Fast and sensitive mapping of nanopore sequencing reads with GraphMap | Nature Communications

https://www.nature.com/articles/ncomms11307
lumpy-sv/extractSplitReads_BwaMem at master · arq5x/lumpy-sv

https://github.com/arq5x/lumpy-sv/blob/master/scripts/extractSplitReads_BwaMem
jts/nanocorrect: Experimental pipeline for correcting nanopore reads

https://github.com/jts/nanocorrect

video - how to install flash plugin on ubuntu 14.04 LTS 64-bit version - Ask Ubuntu

https://askubuntu.com/questions/469553/how-to-install-flash-plugin-on-ubuntu-14-04-lts-64-bit-version
lh3/fermi: A WGS de novo assembler based on the FMD-index for large genomes

https://github.com/lh3/fermi
Multi-metagenome

http://madsalbertsen.github.io/multi-metagenome/docs/step9.html
Bandage by rrwick

https://rrwick.github.io/Bandage/
Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design | Bioinformatics | Oxford Academic

https://academic.oup.com/bioinformatics/article/30/15/2210/2391162
Genome Architecture and Evolution of a Unichromosomal Asexual Nematode - ScienceDirect

https://www.sciencedirect.com/science/article/pii/S096098221731076X?via%3Dihub#fig4
How to determine chimeras in my de novo assembly? - SEQanswers

http://seqanswers.com/forums/showthread.php?t=26721
samtools(1) manual page

http://www.htslib.org/doc/samtools.html
How To Filter Mapped Reads With Samtools

https://www.biostars.org/p/56246/
The MUMmer 3 manual

http://mummer.sourceforge.net/manual/#nucmer
assembly_olc.pdf

http://www.cs.jhu.edu/~langmea/resources/lecture_notes/assembly_olc.pdf
SAM and BAM filtering oneliners

https://gist.github.com/davfre/8596159
Inroduction to dot-plots

http://www.code10.info/index.php%3Foption%3Dcom_content%26view%3Darticle%26id%3D64:inroduction-to-dot-plots%26catid%3D52:cat_coding_algorithms_dot-plots%26Itemid%3D76
RepeatFinder Home Page

http://www.cbcb.umd.edu/software/RepeatFinder/
RepeatFinderReprint.pdf

http://www.cbcb.umd.edu/software/RepeatFinder/RepeatFinderReprint.pdf
https://bernatgel.github.io/karyoploter_tutorial//Tutorial/CreateIdeogram/CreateIdeogram.html

https://bernatgel.github.io/karyoploter_tutorial//Tutorial/CreateIdeogram/CreateIdeogram.html
Circular Visualization in R

http://zuguang.de/circlize_book/book/introduction.html#a-qiuck-glance
Creating a coverage plot using BEDTools and R

https://davetang.org/muse/2015/08/05/creating-a-coverage-plot-using-bedtools-and-r/
Eval: A software package for analysis of genome annotations | BMC Bioinformatics | Full Text

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-4-50
eval-documentation.pdf

http://mblab.wustl.edu/media/software/eval-documentation.pdf
OmicCircos: A Simple-to-Use R Package for the Circular Visualization of Multidimensional Omics Data

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3921174/
sequence - download.tardigrades.org > v1 > sequence

http://download.tardigrades.org/v1/sequence/
ksahlin/BESST: BESST - scaffolder for genomic assemblies

https://github.com/ksahlin/BESST
reubwn/scripts: Useful scripts for various things

https://github.com/reubwn/scripts
ICEberg

http://db-mml.sjtu.edu.cn/ICEberg/index.php
Satsuma - Evolution and Genomics

http://evomics.org/learning/genomics/satsuma/
A complete bacterial genome assembled de novo using only nanopore sequencing data | Nature Methods

https://www.nature.com/articles/nmeth.3444
vezzi/FRC_align: Computes FRC from SAM/BAM file and not from afg files

https://mail.google.com/mail/u/0/#inbox
Read GTF file into R - Dave Tang's blog

https://davetang.org/muse/2017/08/04/read-gtf-file-r/

https://bernatgel.github.io/karyoploter_tutorial//Tutorial/CustomGenomes/CustomGenomes.html

https://bernatgel.github.io/karyoploter_tutorial//Tutorial/CustomGenomes/CustomGenomes.html
Dot: Interactive dot plot for genome-genome alignments

https://dnanexus.github.io/dot/
Zoho Accounts

https://accounts.zoho.eu/signin?servicename=ZohoProjects&serviceurl=https%3A%2F%2Fprojects.zoho.eu%2Fportal%2Favaga2
lh3/minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences

https://github.com/lh3/minimap2
SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information | BMC Bioinformatics | Full Text

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-211
Palindromic gene amplification — an evolutionarily conserved role for DNA inverted repeats in the genome | Nature Reviews Cancer

https://www.nature.com/articles/nrc2591
bioinformatics - BLAST DNA Sequences Reversed - Biology Stack Exchange

https://biology.stackexchange.com/questions/8160/blast-dna-sequences-reversed
LASTZ

http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00a.html
SOGo - (1652) Inbox

https://sogo.unamur.be/SOGo/so/jnarayan/Mail/view
Tetra-Nucleotide Analysis (TNA) | BIOiPLUG Help center

http://help.bioiplug.com/tetra-nucleotide-analysis-tna/

Clustering metagenomic contigs on tetranucleotide frequency — CGAT documentation

http://cgat.readthedocs.io/en/latest/recipes/metagenome_contigs_kmers.html