BOL: Related items

Bambus

Jit — Tue, 16 Aug 2016 08:09:15 -0500

Bambus 2.0, the second generation Bambus scaffolder available as an open source package. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.

Home Page:

http://sourceforge.net/apps/mediawiki/amos/index.php?title=Bambus2

Address of the bookmark: https://www.cbcb.umd.edu/software/bambus2

EasyBuild

Jit — Fri, 27 Jan 2017 16:00:43 -0600

EasyBuild is a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way.
A full list of supported software packages is available here.

Address of the bookmark: https://hpcugent.github.io/easybuild/

WGS Celera Assembler version 8.3rc2

Jit — Mon, 10 Apr 2017 04:45:40 -0500

These are release notes for Celera Assembler version 8.3rc2, which was released on May 24, 2015.

This distribution package provides a stable, tested, documented version of the software. The distribution is usable on most Unix-like platforms, and some platforms have pre-compiled binary distributions ready for installation.

The source code package includes full source code (revision 4627), Makefiles, and scripts. A subset of the kmer package (http://kmer.sourceforge.net/, version r1994), used by some modules of Celera Assembler, is included. This distribution includes [http://samtools.sourceforge.net/ SAMtools], [http://www.cbcb.umd.edu/software/jellyfish/ Jellyfish 2.0], [https://github.com/pbjd/pbutgcns PBUTGCNS], [https://github.com/PacificBiosciences/pbdagcon PBDAGCON], [https://github.com/PacificBiosciences/BLASR BLASR], and parts of the [https://github.com/PacificBiosciences/FALCON/tree/v0.1.3 Falcon assembler].

Full documentation can be found online at http://wgs-assembler.sourceforge.net/.

Interesting scripts within it

urbe@urbo214b[bin] ls []
-rwxrwxr-x 1 urbe urbe 11K Apr 10 11:41 addCNSToStore
-rwxrwxr-x 1 urbe urbe 575K Apr 10 11:41 addReadsToUnitigs
-rwxrwxr-x 1 urbe urbe 128K Apr 10 11:41 analyzeBest
-rwxrwxr-x 1 urbe urbe 257K Apr 10 11:41 analyzePosMap
-rwxrwxr-x 1 urbe urbe 1,5M Apr 10 11:41 analyzeScaffolds
-rwxrwxr-x 1 urbe urbe 224K Apr 10 11:41 asmOutputFasta
-rwxrwxr-x 1 urbe urbe 448K Apr 10 11:41 asmOutputStatistics
-rwxrwxr-x 1 urbe urbe 2,4K Apr 10 11:41 asmToAGP.pl
-rwxrwxr-x 1 urbe urbe 7,6M Apr 10 11:41 blasr
-rwxrwxr-x 1 urbe urbe 1,6M Apr 10 11:41 bogart
-rwxrwxr-x 1 urbe urbe 183K Apr 10 11:41 bogus
-rwxrwxr-x 1 urbe urbe 272K Apr 10 11:41 bogusness
-rwxrwxr-x 1 urbe urbe 247K Apr 10 11:41 buildPosMap
-rwxrwxr-x 1 urbe urbe 213K Apr 10 11:41 buildRefContigs
-rwxrwxr-x 1 urbe urbe 990K Apr 10 11:41 buildUnitigs
-rwxrwxr-x 1 urbe urbe 18K Apr 10 11:41 ca2ace.pl
-rwxrwxr-x 1 urbe urbe 12K Apr 10 11:41 caqc_help.ini
-rwxrwxr-x 1 urbe urbe 61K Apr 10 11:41 caqc.pl
-rwxrwxr-x 1 urbe urbe 23K Apr 10 11:41 cat-corrects
-rwxrwxr-x 1 urbe urbe 24K Apr 10 11:41 cat-erates
-rwxrwxr-x 1 urbe urbe 1,9M Apr 10 11:41 cgw
-rwxrwxr-x 1 urbe urbe 1,4M Apr 10 11:41 cgwDump
-rwxrwxr-x 1 urbe urbe 204K Apr 10 11:41 chimChe
-rwxrwxr-x 1 urbe urbe 201K Apr 10 11:40 chimera
-rwxrwxr-x 1 urbe urbe 220K Apr 10 11:41 classifyMates
-rwxrwxr-x 1 urbe urbe 201K Apr 10 11:41 classifyMatesApply
-rwxrwxr-x 1 urbe urbe 215K Apr 10 11:41 classifyMatesPairwise
-rwxrwxr-x 1 urbe urbe 366K Apr 10 11:41 computeCoverageStat
-rwxrwxr-x 1 urbe urbe 9,8K Apr 10 11:41 convert-fasta-to-v2.pl
-rwxrwxr-x 1 urbe urbe 48K Apr 10 11:41 convertOverlap
-rwxrwxr-x 1 urbe urbe 119K Apr 10 11:41 convertSamToCA
-rwxrwxr-x 1 urbe urbe 20K Apr 10 11:41 convertToPBCNS
-rwxrwxr-x 1 urbe urbe 197K Apr 10 11:41 correct-frags
-rwxrwxr-x 1 urbe urbe 259K Apr 10 11:41 correct-olaps
-rwxrwxr-x 1 urbe urbe 520K Apr 10 11:41 correctPacBio
-rwxrwxr-x 1 urbe urbe 540K Apr 10 11:41 ctgcns
-rwxrwxr-x 1 urbe urbe 162K Apr 10 11:40 deduplicate
-rwxrwxr-x 1 urbe urbe 37K Apr 10 11:41 demotePosMap
-rwxrwxr-x 1 urbe urbe 1,5M Apr 10 11:41 dumpCloneMiddles
-rwxrwxr-x 1 urbe urbe 124K Apr 10 11:41 dumpPBRLayoutStore
-rwxrwxr-x 1 urbe urbe 1,3M Apr 10 11:41 dumpSingletons
-rwxrwxr-x 1 urbe urbe 171K Apr 10 11:41 erate-estimate
-rwxrwxr-x 1 urbe urbe 221K Apr 10 11:40 estimate-mer-threshold
-rwxrwxr-x 1 urbe urbe 1,5M Apr 10 11:41 extendClearRanges
-rwxrwxr-x 1 urbe urbe 1,3M Apr 10 11:41 extendClearRangesPartition
-rwxrwxr-x 1 urbe urbe 205K Apr 10 11:40 extractmessages
-rwxrwxr-x 1 urbe urbe 7,2M Apr 10 11:41 falcon_sense
-rwxrwxr-x 1 urbe urbe 9,8K Apr 10 11:41 fastaToCA
-rwxrwxr-x 1 urbe urbe 124K Apr 10 11:40 fastqAnalyze
-rwxrwxr-x 1 urbe urbe 137K Apr 10 11:40 fastqSample
-rwxrwxr-x 1 urbe urbe 62K Apr 10 11:40 fastqSimulate
-rwxrwxr-x 1 urbe urbe 121K Apr 10 11:40 fastqSimulate-sort
-rwxrwxr-x 1 urbe urbe 246K Apr 10 11:40 fastqToCA
-rwxrwxr-x 1 urbe urbe 140K Apr 10 11:41 filterOverlap
-rwxrwxr-x 1 urbe urbe 341K Apr 10 11:40 finalTrim
-rwxrwxr-x 1 urbe urbe 228K Apr 10 11:41 fixUnitigs
-rwxrwxr-x 1 urbe urbe 147K Apr 10 11:40 fragmentDepth
-rwxrwxr-x 1 urbe urbe 29K Apr 10 11:41 fragsInVars
-rwxrwxr-x 1 urbe urbe 545K Apr 10 11:41 frgs2clones
-rwxrwxr-x 1 urbe urbe 398K Apr 10 11:40 gatekeeper
-rwxrwxr-x 1 urbe urbe 139K Apr 10 11:40 gatekeeperbench
-rwxrwxr-x 1 urbe urbe 167K Apr 10 11:40 gkpStoreCreate
-rwxrwxr-x 1 urbe urbe 147K Apr 10 11:40 gkpStoreDumpFASTQ
-rwxrwxr-x 1 urbe urbe 184K Apr 10 11:41 greedyFragmentTiling
-rwxrwxr-x 1 urbe urbe 1,6K Apr 10 11:41 greedy_layout_to_IUM
-rwxrwxr-x 1 urbe urbe 142K Apr 10 11:40 initialTrim
-rwxrwxr-x 1 urbe urbe 967K Apr 10 11:41 jellyfish
-rwxrwxr-x 1 urbe urbe 219K Apr 10 11:41 markRepeatUnique
-rwxrwxr-x 1 urbe urbe 273K Apr 10 11:40 markUniqueUnique
-rwxrwxr-x 1 urbe urbe 114K Apr 10 11:40 mercy
-rwxrwxr-x 1 urbe urbe 3,8K Apr 10 11:41 mergeqc.pl
-rwxrwxr-x 1 urbe urbe 422K Apr 10 11:40 merTrim
-rwxrwxr-x 1 urbe urbe 125K Apr 10 11:40 merTrimApply
-rwxrwxr-x 1 urbe urbe 376K Apr 10 11:40 meryl
-rwxrwxr-x 1 urbe urbe 176K Apr 10 11:41 metagenomics_ovl_analyses
-rwxrwxr-x 1 urbe urbe 297K Apr 10 11:41 olap-from-seeds
-rwxrwxr-x 1 urbe urbe 275K Apr 10 11:41 outputLayout
-rwxrwxr-x 1 urbe urbe 229K Apr 10 11:41 overlapInCore
-rwxrwxr-x 1 urbe urbe 144K Apr 10 11:40 overlap_partition
-rwxrwxr-x 1 urbe urbe 179K Apr 10 11:41 overlapStats
-rwxrwxr-x 1 urbe urbe 179K Apr 10 11:41 overlapStore
-rwxrwxr-x 1 urbe urbe 153K Apr 10 11:41 overlapStoreBucketizer
-rwxrwxr-x 1 urbe urbe 175K Apr 10 11:41 overlapStoreBuild
-rwxrwxr-x 1 urbe urbe 33K Apr 10 11:41 overlapStoreIndexer
-rwxrwxr-x 1 urbe urbe 48K Apr 10 11:41 overlapStoreSorter
-rwxrwxr-x 1 urbe urbe 604K Apr 10 11:40 overmerry
lrwxrwxrwx 1 urbe urbe 4 Apr 10 11:41 pacBioToCA -> PBcR
-rwxrwxr-x 1 urbe urbe 131K Apr 10 11:41 PBcR
-rwxrwxr-x 1 urbe urbe 2,9M Apr 10 11:41 pbdagcon
-rwxrwxr-x 1 urbe urbe 1,9M Apr 10 11:41 pbutgcns
-rwxrwxr-x 1 urbe urbe 201K Apr 10 11:40 remove_fragment
-rwxrwxr-x 1 urbe urbe 153K Apr 10 11:40 removeMateOverlap
-rwxrwxr-x 1 urbe urbe 2,5K Apr 10 11:41 replaceUIDwithName-fastq
-rwxrwxr-x 1 urbe urbe 1,2K Apr 10 11:41 replaceUIDwithName-posmap
-rwxrwxr-x 1 urbe urbe 1,3M Apr 10 11:41 resolveSurrogates
-rwxrwxr-x 1 urbe urbe 139K Apr 10 11:41 rewriteCache
-rwxrwxr-x 1 urbe urbe 232K Apr 10 11:41 runCA
-rwxrwxr-x 1 urbe urbe 88K Apr 10 11:41 runCA-dedupe
-rwxrwxr-x 1 urbe urbe 14K Apr 10 11:41 runCA-overlapStoreBuild
-rwxrwxr-x 1 urbe urbe 3,6K Apr 10 11:41 run_greedy.csh
-rwxrwxr-x 1 urbe urbe 297K Apr 10 11:40 sffToCA
-rwxrwxr-x 1 urbe urbe 13K Apr 10 11:40 show-corrects
-rwxrwxr-x 1 urbe urbe 557K Apr 10 11:41 splitUnitigs
-rwxrwxr-x 1 urbe urbe 1,4M Apr 10 11:41 terminator
drwxrwxr-x 2 urbe urbe 4,0K Apr 10 11:41 TIGR
-rwxrwxr-x 1 urbe urbe 526K Apr 10 11:41 tigStore
-rwxrwxr-x 1 urbe urbe 35K Apr 10 11:41 tracearchiveToCA
-rwxrwxr-x 1 urbe urbe 35K Apr 10 11:41 tracedb-to-frg.pl
-rwxrwxr-x 1 urbe urbe 44K Apr 10 11:41 trimFastqByQVWindow
-rwxrwxr-x 1 urbe urbe 18K Apr 10 11:40 uidclient
-rwxrwxr-x 1 urbe urbe 589K Apr 10 11:41 unitigger
-rwxrwxr-x 1 urbe urbe 42K Apr 10 11:40 upgrade-v8-to-v9
-rwxrwxr-x 1 urbe urbe 42K Apr 10 11:40 upgrade-v9-to-v10
-rwxrwxr-x 1 urbe urbe 854 Apr 10 11:41 utg2fasta
-rwxrwxr-x 1 urbe urbe 731K Apr 10 11:41 utgcns
-rwxrwxr-x 1 urbe urbe 561K Apr 10 11:41 utgcnsfix

Address of the bookmark: http://wgs-assembler.sourceforge.net/wiki/index.php/Main_Page

NGS teaching material

Jit — Wed, 05 Apr 2017 04:29:06 -0500

High throughput sequencing (HTS) technologies are being applied to a wide range of important topics in biology. However, the analyses of non-model organisms, for which little previous sequence information is available, pose specific problems. This course addresses the specific strengths and weaknesses of alternative HTS technologies, the computational resources needed for HTS, and how to analyze non-model species using HTS. The course consists of a practical training module, HTS bioinformatics training, and lecturing/seminars of HTS approaches specifically targeting non-model organisms.

Address of the bookmark: http://marinetics.org/teaching/hts/Assembly.html

Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome

Jit — Wed, 29 Nov 2017 05:08:53 -0600

Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used for sequencing the S. cerevisiae genome. To make use of these data, we developed a novel open-source hybrid error correction algorithm Nanocorr (https://github.com/jgurtowski/nanocorr) specifically for Oxford Nanopore reads, as existing packages were incapable of assembling the long read lengths (5-50kbp) at such high error rate (between ~5 and 40% error). With this new method we were able to perform a hybrid error correction of the nanopore reads using complementary MiSeq data and produce a de novo assembly that is highly contiguous and accurate: the contig N50 length is more than ten-times greater than an Illumina-only assembly (678kb versus 59.9kbp), and has greater than 99.88% consensus identity when compared to the reference. Furthermore, the assembly with the long nanopore reads presents a much more complete representation of the features of the genome and correctly assembles gene cassettes, rRNAs, transposable elements, and other genomic features that were almost entirely absent in the Illumina-only assembly.

Address of the bookmark: http://schatzlab.cshl.edu/data/nanocorr/

MeDuSa: a multi-draft based scaffolder

Abhimanyu Singh — Wed, 14 Feb 2018 02:49:00 -0600

MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs. MeDuSa formalises the scaffolding problem by means of a combinatorial optimisation formulation on graphs and implements an efficient constant factor approximation algorithm to solve it. In contrast to currently used scaffolders, it does not require either prior knowledge on the microrganisms dataset under analysis (e.g. their phylogenetic relationships) or the availability of paired end read libraries.

Address of the bookmark: https://github.com/combogenomics/medusa

ERGO 2.0 Bioinformatics suites

Jit — Tue, 16 May 2017 08:14:10 -0500

ERGO 2.0 provides a systems biology informatics toolkit centered on comparative genomics to capture, query, and visualize sequenced genomes. Using Igenbio's proprietary algorithms, and the most comprehensive genomic database integrated with the largest collection of microbial metabolic and non-metabolic pathways, ERGO™ assigns functions to genes, integrates genes into pathways, and identifies previously unknown or mischaracterized genes, cryptic pathways, and gene products.

Address of the bookmark: https://www.igenbio.com/ergo/

Senior Bioinformatics Software Developer, Hyderabad, Telangana

Mon, 03 Jul 2017 10:10:31 -0500

DuPont Pioneer is the world leader in plant biotechnology area including discovery, development and delivery of elite crop genetics. DuPont Pioneer is aggressively building Big Data and Predictive Analytics capabilities in order to deliver improved services to our customers. We are currently seeking Senior Bioinformatics Software Developer at the DuPont Knowledge Center in Hyderabad, India for our global Data Science and Informatics group. At DuPont Pioneer, you’ll become part of a work environment that nurtures your interests, ignites your passion, creates opportunities to serve and helps you attain success–both personally and professionally. The hiring level will be commensurate with the level of experience. This is a critical position with the potential to make immediate, significant impact on our business.
The successful candidate will have an extensive background in computer science and bioinformatics through courses or academic degrees, and proven experience in bioinformatics software development. We are looking for those creative, smart, model driven, agile individuals who enjoy giving their all to tackle diverse software needs.
Duties / Responsibilities

Job Qualifications
Education and Experience
• Master Degree in Bioinformatics, Computational biology, Scientific Computing or related field
• 3-5 years of Post-Master’s experience in Bioinformatics software development
• Proven experience developing high throughput bioinformatics applications
Required Competencies
• Strong proven experience in Python programming language in Linux environment
• Proven High Performance computing experience (LSF/SGE/OGE)
• Exposure in code versioning and repository management (GIT/SVN)
• Proven experience in Bioinformatics algorithm development
• Deep understanding in Bioinformatics tools, data types
Desired Competencies
• Familiarity working in a scientific computing environment (NumPy, SciPy, Pandas etc.)
• Familiarity working with Cloud technologies (AWS, Azure)
• Ability to demonstrate solid analytical skills and exceptional attention to detail.
• Experience in relational databases and data structures
• Proven experience working with teams using agile software development methodologies and processes
• Familiarity with Service Oriented Architecture (SOA)
• Familiarity with build tools (Jenkins, make, ANT, Maven)
• Exposure to project management tools (JIRA, Confluence, RED MINE, etc.)

More at http://careers.dupont.com/jobsearch/job-details/senior-bioinformatics-software-developer/012939W-01/

Hapsembler: An Assembler for Highly Polymorphic Genomes

Jit — Tue, 22 May 2018 04:09:53 -0500

Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types of polymorphism. Hapsembler can be used to assemble reads from a variety of platforms including Illumina and Roche/454. http://compbio.cs.toronto.edu/hapsembler/

Address of the bookmark: http://compbio.cs.toronto.edu/hapsembler/

Bioinformatics tools developed for Oxford Nanopore data analysis !

biogeek — Wed, 27 Dec 2017 20:47:30 -0600

MinION is the only portable real-time device for DNA and RNA sequencing. Each consumable flow cell can now generate 10–20 Gb of DNA sequence data. Ultra-long read lengths are possible (hundreds of kb) as you can choose your fragment length. One of the technical advantages of ONT data is the read length, which offers great prospects for genome assembly. Generally, assemblers are based on several different types of algorithms, such as greedy, overlap-layout-consensus (OLC), de Bruijn graph (DBG), and string graph.

List of analysis tools developed for Oxford Nanopore data

BWA
Fast nanopore data tuned alignment tool
https://github.com/lh3/bwa

GraphMap
Mapper for long and error-prone reads
https://github.com/isovic/graphmap

LAST
Nanopore tuned alignment tool
http://last.cbrc.jp/

LINKS
Software tool for long read scaffolding
https://github.com/warrenlr/LINKS/

marginAlign
Tools to align nanopore reads to a reference
https://github.com/benedictpaten/marginAlign

minoTour
Real time analysis tools
http://minotour.nottingham.ac.uk/

nanoCORR
Error-correction tool for nanopore sequence data
https://github.com/jgurtowski/nanocorr

NanoOK
Software for nanopore data, quality and error profiles
https://documentation.tgac.ac.uk/display/NANOOK/NanoOK

Nanopolish
Nanopore analysis and genome assembly software
https://github.com/jts/nanopolish

nanopore
Variant-detection tool for nanopore sequence data
https://github.com/mitenjain/nanopore

Nanocorrect
Error-correction tool for nanopore sequence data
https://github.com/jts/nanocorrect/

npReader
Real-time conversion and analysis of nanopore reads
https://github.com/mdcao/npReader

poRe
Tool for analyzing and visualizing nanopore data
https://sourceforge.net/p/rpore/wiki/Home/

PoreSeq
Error-correction and variant-calling software
https://github.com/tszalay/poreseq

Poretools
Nanopore sequence analysis and visualization software
https://github.com/arq5x/poretools

SSPACE-LongRead
Genome scaffolding tool
http://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE-longread

SMIS
Genome scaffolding tool
https://sourceforge.net/projects/phusion2/files/smis/

List of assemblers for Oxford Nanopore MinION long reads

LQS
DALIGNER, Celera OLC Nanocorrect,
Nanopolish corrector
https://github.com/jts/nanopolish

PBcR
HGAP or BLASR, Celera OLC
PBcR corrector
http://wgs-assembler.sourceforge.net/wiki/index.php/PBcR
–
Canu
MHAP, Celera OLC
Canu corrector
https://github.com/marbl/canu

Falcon
String graph, Celera OLC
Falcon corrector
https://github.com/PacificBiosciences/falcon

Miniasm
OLC
https://github.com/lh3/miniasm

ra-integrate
OLC
https://github.com/mariokostelac/ra-integrate/

ALLPATHS-LG
de Bruijn graph
ALLPATHS-L corrector
https://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12

SPAdes
de Bruijn graph
SPAdes corrector
http://bioinf.spbau.ru/spades