:: DESCRIPTION
GO4genome is a prokaryotic phylogeny based on genome organization.
::DEVELOPER
Computational Protein Design and Evolution at the University of Regensburg
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Mol Evol. 2009 May;68(5):550-62. doi: 10.1007/s00239-009-9233-6.
GO4genome: a prokaryotic phylogeny based on genome organization.
Merkl R, Wiezer A.
:: DESCRIPTION
MDSOutlier is a free, open-source whole-genome case-control association analysis program, designed for systematic removal of outliers to reduce heterogeneity.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Shen Y, Liu Z, Ott J:
Systematic removal of outliers to reduce heterogeneity in case-control association studies.
Hum Hered 2010;70:227-231
:: DESCRIPTION
Sarek is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse, it can work on any species with a reference genome. Sarek can also handle tumour / normal pairs and could include additional relapses.
::DEVELOPER
the Science for Life Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Garcia M, Juhos S, Larsson M, Olason PI, Martin M, Eisfeldt J, DiLorenzo S, Sandgren J, Díaz De Ståhl T, Ewels P, Wirta V, Nistér M, Käller M, Nystedt B.
Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants.
F1000Res. 2020 Jan 29;9:63. doi: 10.12688/f1000research.16665.2. PMID: 32269765; PMCID: PMC7111497.
:: DESCRIPTION
WGSQuikr is a very rapid, whole-genome shotgun metagenomic reconstruction.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2014 Mar 13;9(3):e91784. doi: 10.1371/journal.pone.0091784. eCollection 2014.
WGSQuikr: fast whole-genome shotgun metagenomic classification.
Koslicki D, Foucart S, Rosen G.
:: DESCRIPTION
WGA-LP is a pipeline for whole genome assembly that simplifies the usage of different tools and helps the user in evaluating his results.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Rossi N, Colautti A, Iacumin L, Piazza C.
WGA-LP: a pipeline for Whole Genome Assembly of contaminated reads.
Bioinformatics. 2021 Oct 20:btab719. doi: 10.1093/bioinformatics/btab719. Epub ahead of print. PMID: 34668528.
:: DESCRIPTION
WHAMM is a free, open-source analysis package designed to estimate patterns of homozygosity in whole genome data sets, as well as perform a range of association analyses and summaries on the resultant output.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Celera Assembler (wgs-assembler) is scientific software for DNA research. It can reconstruct long sequences of genomic DNA given the fragmentary data produced by whole-genome shotgun sequencing. The Celera Assembler has enabled discovery in microbial genomes, large eukaryotic genomes, diploid genomes, and genomes from environmental samples. Celera Assembler contributed the first diploid sequence of an individual human, and metagenomics assemblies of the Global Ocean Sampling
Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION).
::DEVELOPER
Celera Assembler team / Maryland Bioinformatics Labs (MarBL)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM.
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
Genome Res. 2017 May;27(5):722-736. doi: 10.1101/gr.215087.116. Epub 2017 Mar 15. PMID: 28298431; PMCID: PMC5411767.
Denisov et al. (2008)
Consensus Generation and Variant Detection by Celera Assembler.
Bioinformatics 24(8):1035-40
:: DESCRIPTION
INTEGRATE is a tool for calling gene fusions with exact fusion junctions and genomic breakpoints by combining RNA-Seq and WGS data.
INTEGRATE-Neo is a tool for gene fusion neoantigen discovering tool using next-generation sequencing data.
::DEVELOPER
The Zhang Translational Genomics Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhang J, Mardis ER, Maher CA.
INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery.
Bioinformatics. 2017 Feb 15;33(4):555-557. doi: 10.1093/bioinformatics/btw674. PMID: 27797777; PMCID: PMC5408800.
Zhang J, White NM, Schmidt HK, Fulton RS, Tomlinson C, Warren WC, Wilson RK, Maher CA.
INTEGRATE: gene fusion discovery using whole genome and transcriptome data.
Genome Res. 2016 Jan;26(1):108-18. doi: 10.1101/gr.186114.114. Epub 2015 Nov 10. PMID: 26556708; PMCID: PMC4691743.
:: DESCRIPTION
AMOS (A Modular, Open-Source) consortium is committed to the development of open-source whole genome assembly software. The project acronym (AMOS) represents our primary goal — to produce A Modular, Open-Source whole genome assembler.Open-source so that everyone is welcome to contribute and help build outstanding assembly tools, and modular in nature so that new contributions can be easily inserted into an existing assembly pipeline. This modular design will foster the development of new assembly algorithms and allow the AMOS project to continually grow and improve in hopes of eventually becoming a widely accepted and deployed assembly infrastructure. In this sense, AMOS is both a design philosophy and a software system.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Next generation sequence assembly with AMOS.
Treangen TJ, Sommer DD, Angly FE, Koren S, Pop M.
Curr Protoc Bioinformatics. 2011 Mar;Chapter 11:Unit 11.8. doi: 10.1002/0471250953.bi1108s33.
:: DESCRIPTION
MIRA (Mimicking Intelligent Read Assembly)is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads). It can be seen as a Swiss army knife of sequence assembly developed and used in the past 12 years to get assembly jobs done efficiently – and especially accurately. That is, without actually putting too much manual work into finishing the assembly.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Chevreux et al. (2004)
Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs
Genome Research 2004. 14:1147-1159.
