Sarek 2.7.1 – Detect Germline or Somatic Variants from Whole Genome or Targeted Sequencing

Sarek 2.7.1

:: 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

  • Linux
  • Docker

:: DOWNLOAD

Sarek

:: 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.

WGSQuikr 1.0.0 – Whole-genome Shotgun Metagenomic Classification

WGSQuikr 1.0.0

:: DESCRIPTION

WGSQuikr is a very rapid, whole-genome shotgun metagenomic reconstruction.

::DEVELOPER

WGSQuikr team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX /Windows
  • MatLab

:: DOWNLOAD

 WGSQuikr

:: 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.

WGA-LP – A Pipeline for Whole Genome Assembly

WGA-LP

:: 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

WGA-LP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

WGA-LP

:: 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.

WHAMM 0.14c – Whole-Genome Homozygosity Analysis and Mapping Machina

WHAMM 0.14c

:: 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

Benjamin F. Voight, PhD

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

   WHAMM

:: MORE INFORMATION

Celera Assembler 8.3 / Canu v2.2 – Whole Genome Shotgun Assembler

Celera Assembler 8.3 / Canu v2.2

:: 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

  • Linux

:: DOWNLOAD

Celera Assembler / Canu

:: 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

INTEGRATE 0.2.6 / INTEGRATE-Neo 1.2.1 – Gene Fusion Discovery using Whole Genome and Transcriptome data

INTEGRATE 0.2.6 / INTEGRATE-Neo 1.2.1

:: 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

  • Linux

:: DOWNLOAD

INTEGRATE / INTEGRATE-Neo

:: 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.

AMOS 3.1.0 – Whole Genome Shotgun Assembler

AMOS 3.1.0

:: 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

AMOS Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

AMOS

:: 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.

MIRA 4.9.6 – Whole Genome Shotgun and EST Sequence Assembler

MIRA 4.9.6

:: 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

Bastien Chevreux

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Mac OsX

:: DOWNLOAD

 MIRA

:: 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.

Satsuma2 – Whole-genome Synteny Aligner

Satsuma2

:: DESCRIPTION

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.

Satsuma2 is an optimised version of Satsuma, a tool to reliably align large and complex DNA sequences providing maximum sensitivity (to find all there is to find), specificity (to only find real homology) and speed (to accomodate the billions of base pairs in vertebrate genomes).

::DEVELOPER

Grabherr Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

Satsuma2

:: MORE INFORMATION

Citation

Grabherr MG, Russell P, Meyer M, Mauceli E, Alfoldi J, Di Palma F, Lindblad-Toh K.
Genome-wide synteny through highly sensitive sequence alignment: Satsuma.
Bioinformatics. 2010 May 1;26(9):1145-51. Epub 2010 Mar 5

Atlas 2005 – Whole Genome Assembly Suite

Atlas 2005

:: DESCRIPTION

Atlas is a collection of software tools to facilitate the assembly of large genomes from whole genome shotgun reads, or a combination of whole genome shotgun reads and BAC or other localized reads.

::DEVELOPER

Human Genome Sequencing Center, Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Atlas

:: MORE INFORMATION