BOL: Related items

Rajiv Gandhi Centre for Biotechnology (RGCB) invites applications for the following three faculty scientist

Tue, 24 Nov 2015 22:13:16 -0600

Scientist Positions
Advt. No.RGCB Advt./SCI 2015/1

November 11, 2015

Rajiv Gandhi Centre for Biotechnology (RGCB) invites applications for the following three faculty scientist positions:

Scientist E-II or F in Bioinformatics & Computational Biology

SCIENTIST E-II OR F IN COMPUTATIONAL BIOLOGY & BIOINFORMATICS

Highly motivated and innovative individual who will pursue basic research, solve biological problems with emphasis on computational and quantitative experimental methods and build active bridges to translational research. The scientist will also provide computational biology support to ongoing research programs in disease biology, provide assistance to analyze complex data sets generated by RGCB scientists and collaborators inclusive of including high dimensional “omics” data and next generation sequencing data, such as whole genome, exome, RNA-seq and ChIP-seq as well as provide leadership for high quality training for junior scientists and regular teaching programs of the institute. Areas of research of interest to RGCB include but are not limited to computational, systems, or quantitative biology with applications to cell biology, developmental biology, metabolism, genomics, proteomics, biophysics, biological information systems, network pharmacology, drug design and cancer research. The scientist’s responsibilities include efforts for the integration of DNA variant annotation with statistical genetic analysis methods including linkage, imputation and association methods, adopting novel and innovative methodologies to analyze, integrate and interpret high dimensional data sets, provision of annotation to robust genetics and genomics findings using several data sources and methods, data management of exploratory clinical and R&D studies in partnership with other lines of genetic data generated from internal and external studies, delivery and documentation of genomic information to support genetic studies, ensuring high-quality genetic and genomic data is incorporated into exploratory- clinical research programs, developing tools that make maximum use of multiple data sources to support annotation of DNA variation and contributes to systems biology initiatives within RGCB

More at http://rgcb.res.in/scientist-positions/

Application Form http://rgcb.res.in/wp-content/uploads/2015/11/APPLICATION-FORMAT-FOR-SCIENTISTS.docx

Pilon

Rahul Nayak — Mon, 08 Feb 2016 15:56:18 -0600

Pilon is a software tool which can be used to:

Automatically improve draft assemblies
Find variation among strains, including large event detection

Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads aligned to the input FASTA file. Pilon uses read alignment analysis to identify inconsistencies between the input genome and the evidence in the reads. It then attempts to make improvements to the input genome, including:

Single base differences
Small indels
Larger indel or block substitution events
Gap filling
Identification of local misassemblies, including optional opening of new gaps

More at https://github.com/broadinstitute/pilon/wiki

Address of the bookmark: https://github.com/broadinstitute/pilon/wiki

Computer simulation of genetic mechanism !!

Jit — Sun, 13 Mar 2016 09:29:56 -0500

Computer simulation is the discipline of designing a model of an actual or theoretical physical/biological system, executing the model on a digital computer, and analyzing the execution output. Simulation embodies the principle of ``learning by doing'' --- to learn about the system we must first build a model of some sort and then operate the model. The use of simulation is an activity that is as natural as a child who role plays. Children understand the world around them by simulating (with toys and figurines) most of their interactions with other people, animals and objects. As adults, we lose some of this childlike behavior but recapture it later on through computer simulation. To understand reality and all of its complexity, we must build artificial objects and dynamically act out roles with them. Computer simulation is the electronic equivalent of this type of role playing and it serves to drive synthetic environments and virtual worlds. Within the overall task of simulation, there are three primary sub-fields: model design, model execution and model analysis

Simulation models have become important tools in Bioinformatics studies. There are many reasons for this, but we emphasize three of the more important:

(1) they enable exploration of hypotheses, and as such, have become invaluable means to guide research;

(2) they are unique approaches to integrate (in the literal term of the word) biological knowledge, in the form of experimental results; and

(3) they enable connecting biology with other fields of study ranging from physiology to genomics;

This blog, and this software list, is intended to guide the potential user of simulation models.
It is not, in any way, meant to be comprehensive on the very diverse simulation tools that already exist, but focuses on mechanistic, dynamic models. Similarly, it is not meant to provide any coverage of the breadth of applications; however, for interested readers, we provide references to use as a possible starting point.

Simulation models are meant to answer questions which scientists have in a dynamic, quantitative, and often, a pictorial way. Much of the bioinformatics research and its applications, in particular, involve a large number of components, actors, and factors. Assembling these in a coherent framework may seem a daunting task, especially for beginners, and can lead to confusion, even for experienced scientists, especially if the objectives of such an exercise are not well defined. Followings are the list of tools bioinformatician may use to analyze and provide answers to complex biological mechanisms and related problems.

Software Resource	Brief Description and Homepage
Aladyn	Tools to investigate how demographic parameters, populations genetics and abiotic conditions affect the rate of adaptation http://www.katja-schiffers.eu/research.html
ALF	A Simulation Framework for Genome Evolution http://www.cbrg.ethz.ch/alf
ART	ART is a set of simulation tools to generate synthetic next-generation sequencing data by mimicking real sequencing process with empirical error models or quality profiles. http://www.niehs.nih.gov/research/resources/software/biostatistics/art/
BAMSurgeon	Methods for realistic simulation of mutations in real data. https://github.com/adamewing/bamsurgeon
Bayesian Serial SimCoal	Bayesian Serial SimCoal, (BayeSSC) is a modification of SIMCOAL 1.0, a program written by Laurent Excoffier, John Novembre, and Stefan Schneider. http://www.stanford.edu/group/hadlylab/ssc/index.html
BaySICS	An integral platform with a graphical interface for statistical inference based on approximate Bayesian computation. https://sites.google.com/site/baysicsabc/
BEERS	BEERS was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data http://cbil.upenn.edu/beers/
BOTTLENECK	Bottleneck is a program for detecting recent effective population size reductions from allele data frequencies http://www.ensam.inra.fr/urlb/bottleneck/bottleneck.html
BottleSim	BottleSim is a computer simulation program for simulating the process of population bottlenecks http://chkuo.name/software/bottlesim.html
CASS	Protein Sequence Simulation https://liberles.cst.temple.edu/software/cass/index.html
CDPOP	CDPOP is a landscape genetics tool for simulating the emergence of spatial genetic structure in populations resulting from specified landscape processes governing organism movement behavior. http://cel.dbs.umt.edu/cdpop
Classical Genetics Simulator	Web-based simulation software http://www.cgslab.com/
CoaSim	CoaSim is a tool for simulating the coalescent process with recombination and geneconversion under various demographic models. http://users-birc.au.dk/mailund/coasim/index.html
cosi	The cosi package is written in C and is available as a tar file. http://www.broadinstitute.org/~sfs/cosi/
CS-PSeq-Gen	A program to simulate the evolution of protein sequences under the constraints of the information of a particular reconstructed phylogeny http://bioserv.rpbs.univ-paris-diderot.fr/software/cs-pseq-gen/
DAWG	An application designed to simulate the evolution of recombinant DNA sequences in continuous time http://scit.us/projects/dawg
Easypop	EASYPOP is an individual based model intended to simulate datasets under a very broad range of conditions http://www.unil.ch/dee/en/home/menuinst/softwares--dataset/softwares/easypop.html
EggLib	EggLib is a C++/Python library and program package for evolutionary genetics and genomics. http://egglib.sourceforge.net/
EpiSIM	EpiSIM: simulation of multiple epistasis, linkage disequilibrium patterns and haplotype blocks for genome-wide interaction analysis https://sourceforge.net/projects/episimsimulator/files/
EvolSimulator	A simulation test bed for hypotheses of genome evolution http://acb.qfab.org/acb/evolsim/
EvolveAGene	A realistic coding sequence simulation program that separates mutation from selection and allows the user to set selection conditions http://bellinghamresearchinstitute.com/software/index.html
fastsimcoal	A continuous-‐time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios http://cmpg.unibe.ch/software/fastsimcoal/
FastSLINK	Simulation of Marker and Phenotype Data in Pedigrees https://watson.hgen.pitt.edu/
FFPopSim	C++/Python library for population genetics. http://webdav.tuebingen.mpg.de/ffpopsim/
FLUX SIMULATOR	The Flux Simulator aims at providing a deterministic in silico reproduction of the experimental pipelines for RNA-Seq, employing a minimal set of parameters. http://sammeth.net/confluence/display/sim/home
forqs	Forward-in-time simulation of Recombination, Quantitative Traits, and Selection https://bitbucket.org/dkessner/forqs
ForSim	ForSim: A Forward Evolutionary Computer Simulation http://anth.la.psu.edu/research/weiss-lab/research/research
ForwSim	The program given below is based on the algorithm described in Padhukasahasram et al. 2008 to simulate genetic drift in a standard Wright-Fisher process. http://badri-populationgeneticsimulators.blogspot.com/
FPG	Forward Population Genetic simulation https://bio.cst.temple.edu/~hey/software/software.htm#fpg
FREGENE	FREGENE is a C++ program that simulates sequence-like data over large genomic regions in large diploid populations. http://www.ebi.ac.uk/projects/bargen
FIGG	FIGG is a genome simulation tool that uses known or theorized variation frequency, per a given fragment size and grouped by GC content across a genome to model new genomes in FASTA format while tracking applied mutations for use in analysis http://insilicogenome.sourceforge.net/
fwdpp	A C++ template library for implementing efficient forward simulations. http://molpopgen.github.io/fwdpp/
GAMETES	Genetic Architecture Model Emulator for Testing and Evaluating Software: Simulates complex SNP models with pure, strict epistatic interactions with n-loci. http://sourceforge.net/projects/gametes/?source=navbar
GASP	Genometric Analysis Simulation Program. A software tool for testing and investigating methods in statistical genetics by generating samples of family data based on user specified models. http://research.nhgri.nih.gov/gasp/
GCTA	Genome-wide Complex Trait Analysis http://www.complextraitgenomics.com/software/gcta/download.html
GemSIM	Next generation sequencing read simulator http://sourceforge.net/projects/gemsim/
GeneArtisan	Simulation of Markers in Case-Control Study Designs http://www.rannala.org/?page_id=241
GENOME	A rapid coalescent-based whole genome simulator http://www.sph.umich.edu/csg/liang/genome/
GenomePop2	GenomePop2 is a specialization of the program GenomePop just to manage SNPs under more flexible and useful settings. If you need models with more than 2 alleles please use the GenomePop program version. https://ritchielab.psu.edu/research/research-areas/statistical-genetics-and-gen-epi/methods/genomesimla
GenomeSimla	GenomeSIMLA is currently under development- however, we have a beta release that we are asking to be tested http://chgr.mc.vanderbilt.edu/genomesimla/
GENS2	Simulates interactions among two genetic and one environmental factor and also allows for epistatic interactions. https://sourceforge.net/projects/gensim/
GWAsimulator	A rapid whole genome simulation program http://biostat.mc.vanderbilt.edu/wiki/main/gwasimulator
HAP-SAMPLE	An association simulator for candidate regions or genome scans http://www.hapsample.org/
HAPGEN	A simulator for the simulation of case control datasets at SNP markers https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html
HapSim	A simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients http://cran.r-project.org/web/packages/hapsim/index.html
HAPSIMU	A program that simulates heterogeneous populations with various known and controllable structures under the continuous migration model or the discrete model http://l.web.umkc.edu/liujian/
IBDsim	IBDSim is a computer package for the simulation of genotypic data under general isolation by distance models. http://raphael.leblois.free.fr/
indel-Seq-Gen	A biological sequence simulation program that simulates highly divergent DNA sequences and protein superfamilies http://bioinfolab.unl.edu/~cstrope/isg/
Indelible	A powerful and flexible simulator of biological evolution http://abacus.gene.ucl.ac.uk/software/indelible/
invertFREGENE	InvertFREGENE is a forward-in-time simulator of inversions in population genetic data http://www.ebi.ac.uk/projects/bargen/
kernalPop	A spatially explicit population genetic simulation engine http://cran.r-project.org/src/contrib/archive/kernelpop/
MaCS	Markovian Coalescent Simulator http://www-hsc.usc.edu/~garykche/
Marlin	Marlin provides a user-friendly interface for performing forward-in-time population genetic simulations. http://www.patrickmeirmans.com/software/marlin.html
Mason	A package for the simulation of nucleotide data. http://www.seqan.de/projects/mason/
mbs	modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection http://www.sendou.soken.ac.jp/esb/innan/innanlab/software.html
Mendel's Accountant	Mendel's Accountant (MENDEL) is an advanced numerical simulation program for modeling genetic change over time and was developed collaboratively by Sanford, Baumgardner, Brewer, Gibson and ReMine http://mendelsaccount.sourceforge.net/
MetaPopGen	Simulates genetics in large size metapopulations https://sites.google.com/site/marcoandrello/metapopgen
MetaSim	A tool to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets http://ab.inf.uni-tuebingen.de/software/metasim/
mlcoalsim	Multilocus Coalescent Simulations http://code.google.com/p/mlcoalsim-v1/
ms	The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets. http://home.uchicago.edu/~rhudson1/source/mksamples.html
msHOT	The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets. http://home.uchicago.edu/~rhudson1/
msms	A coalescent Simlation tool with selection. http://www.mabs.at/ewing/msms/index.shtml
MySSP	A program for the simulation of DNA sequence evolution across a phylogenetic tree http://www.rosenberglab.net/software.html
Nemo	A forward-time, individual-based, genetically explicit, and stochastic simulation program designed to study the evolution of genetic markers, life history traits, and phenotypic traits in a flexible (meta-)population framework. http://nemo2.sourceforge.net/
NetRecodon	Coalescent simulation of coding DNA sequences with recombination (inter and intracodon), migration and demography http://code.google.com/p/netrecodon/
OncoSimulR	BioConductor package for Forward Genetic Simulation of Cancer Progresion with Epistasis https://github.com/rdiaz02/oncosimul
PEDAGOG	Software for simulating eco-evolutionary population dynamics https://bcrc.bio.umass.edu/pedigreesoftware/node/5
phenosim	A tool to add phenotypes to simulated genotypes http://evoplant.uni-hohenheim.de/doku.php?id=software:software
PhyloSim	An R package for the Monte Carlo simulation of sequence evolution http://www.ebi.ac.uk/goldman-srv/phylosim/
pIRS	Profile-based Illumina pair-end reads simulator https://code.google.com/p/pirs/
ProteinEvolver	Simulation of protein evolution along phylogenies under structure-based substitution models http://code.google.com/p/proteinevolver/
QMSim	QTL and Marker Simulator http://www.aps.uoguelph.ca/~msargol/qmsim/
quantiNEMO	An individual-based program for the analysis of quantitative traits with explicit genetic architecture potentially under selection in a structured population http://www2.unil.ch/popgen/softwares/quantinemo/
RECOAL	Simulates new haplotype data from a reference population of haplotypes. ftp://popgen.usc.edu/
Recodon	Coalescent simulation of coding DNA sequences with recombination, migration and demography http://code.google.com/p/recodon/
rlsim	A package for simulating RNA-seq library preparation with parameter estimation http://bit.ly/rlsim-git
Rmetasim	Rmetasim is a front-end for the metasim engine that is implemented as a package that runs in the statistical computing environment R http://cran.r-project.org/web/packages/rmetasim/index.html
RNA Seq Simulator	RSS takes SAM alignment files from RNA-Seq data and simulates over dispersed, multiple replica, differential, non-stranded RNA-Seq datasets. http://useq.sourceforge.net/cmdlnmenus.html#rnaseqsimulator
Rose	Random model of sequence evolution http://bibiserv.techfak.uni-bielefeld.de/rose/
scrm	A coalescent simulator optimized for long sequences and large samples. https://scrm.github.io/
SelSim	SelSim is a program for Monte Carlo simulation of DNA polymorphism data for a recom- bining region within which a single bi-allelic site has experienced natural selection http://www.well.ox.ac.uk/~spencer/selsim/
Seq-Gen	An application for the Monte Carlo simulation of molecular sequence evolution along phylogenetic trees. http://tree.bio.ed.ac.uk/software/seqgen/
SEQPower	Statistical power analysis for sequence-based association studies http://bioinformatics.org/spower/
SeqSIMLA	SeqSIMLA can simulate sequence data with user-specified disease and quantitative trait models. Family or unrelated case-control data can be simulated. http://seqsimla.sourceforge.net/
Serial NetEvolve	A flexible utility for generating serially-sampled sequences along a tree or recombinant network http://biorg.cis.fiu.edu/sne/
SFS_CODE	SFS_CODE can perform forward population genetic simulations under a general Wright-Fisher model with arbitrary migration, demographic, selective, and mutational effects. http://sfscode.sourceforge.net/sfs_code/index/index.html
SIBSIM	Quantitative phenotype simulation in extended pedigrees http://sourceforge.net/projects/sibsim/
SimAdapt	A spatially explicit, individual-based, forward-time, landscape-genetic simulation model combined with a landscape cellular automaton. https://www.openabm.org/model/3137
SIMCOAL2	A coalescent program for the simulation of complex recombination patterns over large genomic regions under various demographic models http://cmpg.unibe.ch/software/simcoal2/
SimCopy	An R package simulating the evolution of copy number profiles along a tree. http://bit.ly/simcopy
SIMLA	SIMLA is a SIMuLAtion program that generates data sets of families for use in Linkage and Association studies. http://dmpi.duke.edu/simla-simulation-software-version-32
SimPed	A Simulation Program to Generate Haplotype and Genotype Data for Pedigree Structures http://bioinformatics.org/simped/
Simprot	A program to simulate protein evolution by substitution, insertion and deletion http://www.uhnresearch.ca/labs/tillier/software.htm#3
SimRare	Rare variant simulation and analysis tool http://code.google.com/p/simrare/
simuGWAS	A forward-time simulator that simulates realistic samples for genome-wide association studies. http://simupop.sourceforge.net/cookbook/simugwas
simuPOP	simuPOP is a general-purpose individual-based forward-time population genetics simulation environment. http://simupop.sourceforge.net/
SISSI	A software tool to generate data of related sequences along a given phylogeny, taking into account user defined system of neighbourhoods and instantaneous rate matrices. http://www.cibiv.at/software/sissi/
SMARTPOP	Simulating Mating Alliance as a Reproductive Tactic for Populations http://smartpop.sourceforge.net/
SNPsim	Coalescent simulation of hotspot recombination http://code.google.com/p/phylosoftware/
SPIP	SPIP simulates the transmission of genes from parents to offspring in a population having demographic structure defined by the user http://swfsc.noaa.gov/textblock.aspx?division=fed&id=3434
Splatche	Spatial and Temporal Coalescences in Heterogeneous Environment http://www.splatche.com/
srv	Simulator of Rare Varaints (srv) is a simulator for the simulation of the introduction and evolution of (rare) genetic variants. http://simupop.sourceforge.net/cookbook/simurarevariants
SUP	SLINK/FastSLINK utility program http://mlemire.freeshell.org/software.html
TreesimJ	A flexible, forward-time population genetic simulator http://code.google.com/p/treesimj/
Variant Simulation Tools	A simulation tool for post-GWAS genetic epidemiological studies using whole-genome or whole-exome next-gen sequencing data, with an emphasis on user-friendliness and reproducibility. http://varianttools.sourceforge.net/simulation/homepage
Vortex	VORTEX is an individual-based simulation model for population viability analysis (PVA). http://www.vortex9.org/vortex.html
Wessim	Whole Exome Sequencing SIMulator http://sak042.github.io/wessim/

PAired-eND Assembler for DNA sequences

Neel — Wed, 06 Apr 2016 05:25:34 -0500

PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

More at https://github.com/neufeld/pandaseq

Address of the bookmark: https://github.com/neufeld/pandaseq

Understanding Fastqc Output

Jit — Fri, 15 Apr 2016 05:47:40 -0500

Understanding Following table and graphs

Duplication level
kmer profile
per base GC content
per base N content
per base quality
per base sequence content
per sequence GC content
per sequence quality
sequence length distribution

More at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/

Address of the bookmark: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/

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

Anjana — Tue, 10 May 2016 07:46:24 -0500

High-throughput genomics has revolutionized biological research, however, while the number of sequenced genomes grows by the day, quality assessment of the resulting assembled sequences remains complicated and mostly limited to technical measures like N50.
BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.
BUSCO assessments are implemented in open-source software, with comprehensive lineage-specific sets of Benchmarking Universal Single-Copy Orthologs for arthropods, vertebrates, metazoans, fungi, eukaryotes, and bacteria.
These conserved orthologs are ideal candidates for large-scale phylogenomics studies, and the annotated BUSCO gene models built during genome assessments provide a comprehensive gene predictor training set for use as part of genome annotation pipelines.
BUSCO assessments offer intuitive metrics, based on evolutionarily informed expectations of gene content from hundreds of species, to gauge completeness of rapidly accumulating genomic data and satisfy an Iberian's quest for quality - "Busco calidad/qualidade".

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

mrFAST: Micro Read Fast Alignment Search Tool

Neel — Tue, 26 Apr 2016 03:50:06 -0500

mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold, including indels up to 4+4 bp. This manual, describes how to choose the parameters and tune mrFAST with respect to the library settings. mrFAST is designed to find 'all' mappings for a given set of reads, however it can return one "best" map location if the relevant parameter is invoked.

More at http://mrfast.sourceforge.net/manual.html

Address of the bookmark: http://mrfast.sourceforge.net/manual.html

GATB : Genome Analysis Toolbox with de-Bruijn graph

Jit — Thu, 28 Apr 2016 11:16:51 -0500

The Genome Analysis Toolbox with de-Bruijn graph (GATB) provides a set of highly efficient algorithms to analyse NGS data sets. These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organisms such as bacteria, plants, animals and even complex samples (e.g. metagenomes).

More at https://gatb.inria.fr/

Address of the bookmark: https://gatb.inria.fr/

SATSUMA : Highly sensitive whole-genome synteny alignments.

Jit — Fri, 13 May 2016 05:25:26 -0500

Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only the parts that are orthologous, i.e. following the conserved order and orientation of features, such as protein coding genes, non-coding genes, or neutral sequences. Satsuma does not require any pre-processing, such as repeat masking, since it will automatically detect ambiguous mappings.

Satsuma has parallelization built-in and is designed to run on multi-core architectures. The run-time for aligning two bird-size genomes (~1.2 Gb) is around two days on 24 CPUs.

You can find the manual here.
Download the latest source code from here.
Stable versions can also be downloaded from the Broad Institute's web site.

An incomplete list of questions and answers (yes, these have really been asked by our users! Please feel free to add your own by e-mailing us) is here.

If you use Satsuma in your research, please cite:
Grabherr, M. G., Russell, P., Meyer, M., Mauceli, E., Alföldi, J., Di Palma, F., & Lindblad-Toh, K. (2010). Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics, 26(9), 1145-51.

Tutorial at http://evomics.org/learning/genomics/satsuma/

Address of the bookmark: http://satsuma.sourceforge.net/

BBMap/BBTools package: Multipurpose tool designed for converting reads or other nucleotide data between different formats.

Jit — Mon, 13 Jun 2016 05:47:21 -0500

Reformatis a member of the BBMap/BBTools package. It is a multipurpose tool designed for converting reads or other nucleotide data between different formats. It supports, and can inter-convert:

fastq
fasta
fasta+qual
sam
scarf (an old Illumina format)
bam (if samtools is installed)
gzip
zip
ascii-33 (sanger)
ascii-64 (old Illumina)
paired files
interleaved files

It is multithreaded and can process data at over 500 megabytes per second, and can accept streams from standard in and write to standard out, allowing it to be easily dropped into the middle of a pipeline for format conversion. Reformat autodetects formats based on file extensions and content, making it very easy to use; and the autodetection can be overridden, allowing flexibility for people who don't like to follow naming conventions, or out-of-spec fastq files with qualities values like -17 or 120.

The program has been gradually expanded, and can now perform various other functions. None of these will break pairing, if the input is paired.

Quality trimming (either or both ends)
Quality filtering
Fixed-length trimming
Generation of histograms (base composition, quality, etc)
Subsampling (to a fraction of input reads, or an exact number of reads or bases)
Changing fasta line-wrapping length
Reverse-complementing (all reads or only read 2)
Adding /1 and /2 suffix to read names
GC-content filtering
Length-filtering
Testing for corrupted interleaved files

Reformat is compatible with any platform that supports Java 1.7 or higher. It also has a bash shellscript for simpler invocation. Typical usage examples:

Reformat fastq into fasta:
reformat.sh in=x.fq out=y.fa

Interleave paired reads:
reformat.sh in1=x1.fq in2=x2.fq out=y.fq

Note - you can actually use a shortcut if paired read files have the same name with a 1 and a 2. This is equivalent to the above command:
reformat.sh in=x#.fq out=y.fq

De-interleave reads:
reformat.sh in=x.fq out1=y1.fq out2=y2.fq

Verify that interleaving appears correct, assuming Illumina namimg conventions:
reformat.sh in=x.fq vint

Convert ASCII-33 to ASCII-64:
reformat.sh in=x.fq out=y.fq qin=33 qout=64

Quality-trim paired reads to Q10 on the left and right ends and discard reads shorter than 50bp after trimming:
reformat.sh in1=x1.fq in2=x2.fq out1=y1.fq out2=y2.fq outsingle=singletons.fq qtrim=rl trimq=10 minlength=50

Subsample 10% of the first 20000 pairs in an interleaved file:
reformat.sh in=x.fq out=y.fq reads=20000 samplerate=0.1 int=t
(in this case "int=t" overrides interleaving autodetection, to ensure reads are treated as pairs)

Pipe in a gzipped sam file and pipe out fasta:
reformat.sh in=stdin.sam.gz out=stdout.fa

Reverse-complement reads:
reformat.sh in=x.fq out=y.fq rcomp

For reformatting a file with very long sequences, Reformat will need more memory; just add the additional flag "-Xmx2g". For example, to change the line-wrapping length on the human genome (which has individual sequences over 200Mbp long) to 70 characters:
reformat.sh -Xmx2g in=HG19.fa.gz out=HG19_wrapped.fa.gz fastawrap=70

For additional functions, please run the shellscript with no arguments, or just read it with a text editor. If you have any questions, please post them in this thread.

For people using a non-bash terminal, you may need to type "bash reformat.sh" instead of just "reformat.sh".
For users of Windows or other platforms that do not support bash shellscripts, replace "reformat.sh" with "java -ea -Xmx200m /path/to/bbmap/current/ jgi.ReformatReads"
for example,
java -ea -Xmx200m C:\bbmap\current\ jgi.ReformatReads in=x.fq out=y.fa

Reformat can be downloaded with BBTools here:
https://sourceforge.net/projects/bbmap/