<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/36884?offset=140 https://bioinformaticsonline.com/bookmarks/view/32131/wgs-celera-assembler-version-83rc2 Mon, 10 Apr 2017 04:45:40 -0500 https://bioinformaticsonline.com/bookmarks/view/32131/wgs-celera-assembler-version-83rc2 <![CDATA[WGS Celera Assembler version 8.3rc2]]> 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

]]> Jit https://bioinformaticsonline.com/bookmarks/view/33011/grinder-biogrinder-a-versatile-omics-shotgun-and-amplicon-sequencing-read-simulator Wed, 24 May 2017 08:41:41 -0500 https://bioinformaticsonline.com/bookmarks/view/33011/grinder-biogrinder-a-versatile-omics-shotgun-and-amplicon-sequencing-read-simulator <![CDATA[Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator]]> Grinder is a versatile program to create random shotgun and amplicon sequence libraries based on DNA, RNA or proteic reference sequences provided in a FASTA file.

Grinder can produce genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, metaproteomic shotgun and amplicon datasets from current sequencing technologies such as Sanger, 454, Illumina. These simulated datasets can be used to test the accuracy of bioinformatic tools under specific hypothesis, e.g. with or without sequencing errors, or with low or high community diversity. Grinder may also be used to help decide between alternative sequencing methods for a sequence-based project, e.g. should the library be paired-end or not, how many reads should be sequenced.

Address of the bookmark: https://sourceforge.net/projects/biogrinder/files/biogrinder/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/43048/coverm-read-coverage-calculator-for-metagenomics Thu, 29 Apr 2021 23:39:14 -0500 https://bioinformaticsonline.com/bookmarks/view/43048/coverm-read-coverage-calculator-for-metagenomics <![CDATA[CoverM: Read coverage calculator for metagenomics]]> CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications.

CoverM calculates coverage of genomes/MAGs coverm genome (help) or individual contigs coverm contig (help). Calculating coverage by read mapping, its input can either be BAM files sorted by reference, or raw reads and reference genomes in various formats.

Address of the bookmark: https://github.com/wwood/CoverM

]]> Neel https://bioinformaticsonline.com/bookmarks/view/38172/bamview-a-free-interactive-display-of-read-alignments-in-bam-data-files Fri, 09 Nov 2018 13:43:22 -0600 https://bioinformaticsonline.com/bookmarks/view/38172/bamview-a-free-interactive-display-of-read-alignments-in-bam-data-files <![CDATA[BamView: a free interactive display of read alignments in BAM data files]]> To run the application on UNIX from the downloaded jar file run the UNIX:

java -mx512m -jar BamView.jar

and extra command line options are given when '-h' is used:

java -jar BamView.jar -h

BAM files can be specified on the command line with the '-a' option:

java -mx512m -jar BamView.jar -a pathToFile/sorted.bam

If a BAM filename is not given on the command line BamView will prompt for a file to be entered. The BAM index file should have the same name as the BAM file but with a '.bai' suffix. Multiple BAM files can be loaded and overlaid in the viewer. To make this easier BamView will read in files that contain a list of filenames.

 

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

]]> Neel https://bioinformaticsonline.com/blog/view/43983/must-read-paper-and-books-in-evolution-biology Wed, 05 Oct 2022 18:33:01 -0500 https://bioinformaticsonline.com/blog/view/43983/must-read-paper-and-books-in-evolution-biology <![CDATA[Must read paper and books in evolution biology !]]> 1. *Nick Barton:* - The textbook "Evolution" by Nick Barton, with resources for exploring the literature: Barton, N. H., Briggs, D. E. G., Eisen, J. A., Goldstein, D. B., & Patel, N. H. (2007). Evolution. Cold Spring Harbor Laboratory Press. - Papers from a course named "Classics in Evolutionary Biology": Evolutionary Synthesis 1. Haldane, J. B. S. 1932. The causes of evolution. Longmans. New York. (esp. Ch. IV). 2. Fisher, R. A. 1930. The genetical theory of natural selection. Oxford University Press, Oxford. Selected Sections - Fundamental Theorem. Genetic Variation 1a. Lewontin, R. C., and J. L. Hubby. 1966. A molecular approach to the study of genic heterozygosity in natural populations. II. Amount of variation and degree of heterozygosity in natural populations of Drosophila pseudoobscura. Genetics. 54:595-609. 1b. Sachidandam et al. 2001. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. 409: 928-33. 2. Wright S., Dobzhansky T., Hovanitz W. 1942 Genetics of natural populations VII The allelism of lethals in the third chromosome of Drosophila pseudoobscura. Genetics 27: 363-394. Recombination and evolution 1. Hill, W. G., and A. Robertson. 1966. The effect of linkage on limits to artificial selection. Genet. Res. 8:269-294. 2. Maynard Smith and Haigh. 1974. The hitch-hiking effect of a favourable gene. Genet. Res. 23: 23-35. Understanding sequence variation 1. Begun D. J., Aquadro C. F., 1992 Levels of naturally occurring DNA polymorphism correlate with recombination rate in Drosophila melanogaster. Nature 356: 519-520. 2. Green R. E., Reich D., Pääbo S., 2010 A draft sequence of the Neandertal genome. Science 328: 710-722. Quantitative Genetics: variation in complex traits 1. Galton F., 1877 Typical laws of heredity. Nature 15: 492-495- 512-514- 532-533. 2. Turelli M., 1984 Heritable genetic variation via mutation-selection balance: Lerch's Zeta meets the abdominal bristle. Theor. Popul. Biol. 25: 138-193. Quantitative Genetics: finding the genes 1. Shrimpton A. E., Robertson A., 1988 The Isolation of polygenic factors controlling bristle score in Drosophila melanogaster II Distribution of third chromosome bristle effects within chromosome sections. Genetics 118: 445-459. 2. Boyle E. A., Li Y. I., Pritchard J. K., 2017 An expanded view of complex traits: from polygenic to omnigenic. Cell 169: 1177-1186. Neutral Evolution 1. Kimura, M. 1968. Evolutionary rate at the molecular level. Science. 217:624-626. 2a. Kern A. D., Hahn M. W., 2018 The Neutral Theory in Light of Natural Selection. Molecular Biology and Evolution 110: 21077-6. 2b. Jensen J. D., Payseur B. A., Stephan W., Aquadro C. F., Lynch M., Charlesworth D., Charlesworth B., 2018 The importance of the Neutral Theory in 1968 and 50 years on: a response to Kern and Hahn 2018. Evolution 112: 2109-4. 2c. Ellegren & Galtier. 2016. Determinants of genetic diversity. Nature Reviews Genetics. Mutation and Genetic Variability 1. Luria, S. E., and M. Delbrück. 1943. Mutations of Bacteria from Virus Sensitivity to Virus Resistance. Genetics. 28(6):491-511. 2. Hill, W G. 1982. "Rates of Change in Quantitative Traits From Fixation of New Mutations." Proceedings of the National Academy of Sciences (U.S.A.) 79: 142-45. Testing for selection 1. McDonald & Kreitman. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature. 2. Begun, et al. Mol. Biol. Evol. 16, 1816-1819 (1999). 3. Siddiq et al. 2016. Experimental test and refutation of a classic case of molecular adaptation in Drosophila melanogaster. Nature Ecology & Evolution. The shifting balance 1. Wright, S. 1932. The roles of mutation, inbreeding, crossbreeding and selection in evolution. Proceedings of the VI International Congress of Genetics: 1. pp 356-366. 2. Coyne, J.A., N.H. Barton, and M. Turelli. 1997. A critique of Wright's shifting balance theory of evolution. Evolution 51: 643-671. 3. Barton. 2016. Sewall Wright on Evolution in Mendelian Populations and the "Shifting Balance". Genetics. Evolution of Sex 1. Muller, H.J. 1964. The relation of recombination to mutational advance. Mutation Res. 1(1):2-9 2. McDonald et al. 2016. Sex speeds adaptation by altering the dynamics of molecular evolution. Nature. Kin Selection, Cooperation, and Conflict 1. Hamilton, W. D. 1964. The genetical evolution of social behaviour I. Journal of Theoretical Biology. 7:1-52. 2. Trivers, R. L. 1974 Parent-offspring conflict. American Zoologist. 14(1):249-264. Sexual Selection 1. Zahavi, A. 1975. Mate selection - a selection of a handicap. J. Theor. Biol. 53:205-214. 2. Kirkpatrick, M., and Ryan, M.J. 1991. The evolution of mating preferences and the paradox of the lek. Nature. 350:33-38. Fitness Landscapes 1. Dean, A. 1995. A Molecular Investigation of Genotype by Environment Interactions. Genetics. 139:19-33. 2. Costanzo et al. 2010. The Genetic Landscape of a Cell. Science. Speciation 1. Coyne, J. A., and H. A. Orr. 1989. Patterns of speciation in Drosophila. Evolution. 43:362-381. 2. Corbett-Detig et al. 2013. Genetic incompatibilities are widespread within species. Nature. 2. *Marcos Antezana:* Valen, L. v. 1975. Energy and Evolution. University of Chicago, Department of Biology. 3. *Remco Folkertsma:* 1. The work by Hopi Hoekstra on local adaptation and oldfield mice 2. Poelstra, J. W., Vijay, N., Bossu, C. M., Lantz, H., Ryll, B., Müller, I., ... & Wolf, J. B. (2014). The genomic landscape underlying phenotypic integrity in the face of gene flow in crows. Science, 344(6190), 1410-1414. 4. *Joshka Kaufmann and Leslie Turner* They offer us a link to 'papers every evolutionary biologist should read', the papers are collected by Leslie Turner. https://static1.squarespace.com/static/53e8cb7ce4b02c4bc3aeeee4/t/5ab8fcb670a6ad55c67fcdf4/1522072758665/EvoBioClassicsRefList.pdf 5. *Sarah Stockwell* Matt Ridley collected classic papers in evolutionary biology and printed part of these papers in his book Evolution (see Matt Ridley. Evolution (Univ. of Oxford Press, 2nd edition, 2004))]]> Abhi https://bioinformaticsonline.com/bookmarks/view/36257/aligngraph-algorithm-for-secondary-de-novo-genome-assembly-guided-by-closely-related-references Tue, 17 Apr 2018 16:21:20 -0500 https://bioinformaticsonline.com/bookmarks/view/36257/aligngraph-algorithm-for-secondary-de-novo-genome-assembly-guided-by-closely-related-references <![CDATA[AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references]]> AlignGraph is a software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism.

Using AlignGraph

AlignGraph --read1 reads_1.fa --read2 reads_2.fa --contig contigs.fa --genome genome.fa --distanceLow distanceLow --distanceHigh distancehigh --extendedContig extendedContigs.fa --remainingContig remainingContigs.fa [--kMer k --insertVariation insertVariation --coverage coverage --part p --fastMap --ratioCheck --iterativeMap --misassemblyRemoval --resume]

 

Address of the bookmark: https://github.com/baoe/AlignGraph

]]> Manisha Mishra https://bioinformaticsonline.com/bookmarks/view/38445/orthoani-an-improved-algorithm-and-software-for-calculating-average-nucleotide-identity Wed, 12 Dec 2018 08:36:08 -0600 https://bioinformaticsonline.com/bookmarks/view/38445/orthoani-an-improved-algorithm-and-software-for-calculating-average-nucleotide-identity <![CDATA[OrthoANI: An improved algorithm and software for calculating average nucleotide identity]]> OAT uses OrthoANI to measure the overall similarity between two genome sequences. ANI and OrthoANI are comparable algorithms: they share the same species demarcation cut-off at 95~96% and large comparison studies have demonstrated both algorithms to produce near identical reciprocal similarities. Details of the OrthoANI algorithm is given in (Lee et al. 2015). OAT employs an easy-to-follow Graphical User Interface that allow researchers to calculate OrthoANI values between genomes of interest without unfamiliar Command Line Environments. Moreover, the OAT_cmd command-line software can be integrated into preexisting bioinformatics pipelines. 

Address of the bookmark: https://www.ezbiocloud.net/tools/orthoani

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/41910/the-wavefront-alignment-wfa-algorithm Sun, 28 Jun 2020 10:17:50 -0500 https://bioinformaticsonline.com/bookmarks/view/41910/the-wavefront-alignment-wfa-algorithm <![CDATA[The wavefront alignment (WFA) algorithm]]> The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage of
homologous regions between the sequences to accelerate the alignment process. As opposed to traditional dynamic programming algorithms that run in quadratic time, the WFA runs in time O(ns), proportional to the read length n and the alignment score s, using O(s^2) memory. Moreover, the WFA exhibits simple data dependencies that can be easily vectorized, even by the automatic features of modern compilers, for different architectures, without the need to adapt the code.

Address of the bookmark: https://github.com/smarco/WFA

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/34565/fogsaa-fast-optimal-global-sequence-alignment-algorithm Fri, 08 Dec 2017 14:41:08 -0600 https://bioinformaticsonline.com/bookmarks/view/34565/fogsaa-fast-optimal-global-sequence-alignment-algorithm <![CDATA[FOGSAA: Fast Optimal Global Sequence Alignment Algorithm]]> Sequence alignment algorithms are widely used to infer similarirty and the point of differences between pair of sequences. FOGSAA is a fast Global alignment algorithm. It is basically a branch and bound approach which starts branch expansion in a greedy way taking the symbols from the given pair of sequences (protein or nucleotide) and results in an optimal alignment faster than conventional dymanic programming techniques. It is also better than the heuristic methods with respect to alignment quality.

Address of the bookmark: http://www.isical.ac.in/~bioinfo_miu/FOGSAA.htm

]]> Jit https://bioinformaticsonline.com/bookmarks/view/34292/automatic-filtering-trimming-error-removing-and-quality-control-for-fastq-data Mon, 13 Nov 2017 05:10:23 -0600 https://bioinformaticsonline.com/bookmarks/view/34292/automatic-filtering-trimming-error-removing-and-quality-control-for-fastq-data <![CDATA[Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data]]> Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fastq file/pair.
Currently it supports processing data from HiSeq 2000/2500/3000/4000, Nextseq 500/550, MiniSeq...and other Illumina 1.8 or newer formats

Address of the bookmark: https://github.com/OpenGene/AfterQC

]]> Rahul Nayak