PANDASEQ 2.11 / Pandaseq-sam 1.4 – PAired-eND Assembler for DNA sequences

PANDASEQ 2.11 / Pandaseq-sam 1.4

:: DESCRIPTION

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

PANDASEQ-SAM is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. This version works on SAM/BAM formatted files.

::DEVELOPER

Neufeld Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX/ Windows
  • C Compiler 

:: DOWNLOAD

 PANDASEQ , PANDASEQ-SAM

:: MORE INFORMATION

Citation

Andre P Masella, Andrea K Bartram, Jakub M Truszkowski, Daniel G Brown and Josh D Neufeld.
PANDAseq: paired-end assembler for illumina sequences.
BMC Bioinformatics 2012, 13:31.

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.

Cufflinks 2.2.1 – Transcript Assembler & Abundance Estimator for RNA-Seq

Cufflinks 2.2.1

:: DESCRIPTION

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.

::DEVELOPER

Cole Trapnell’s lab at the University of Washington.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

Cufflinks

:: MORE INFORMATION

Citation

Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L.
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

Nature Biotechnology doi:10.1038/nbt.1621

DISCOVAR 51750 – Genome Shotgun Assembler and Variant Caller

DISCOVAR 51750

:: DESCRIPTION

DISCOVAR is a whole genome shotgun assembler and variant caller that can generate high quality assemblies and variant calls from the latest 250 base Illumina PCR-free fragment reads.

::DEVELOPER

Computational Research and Development Group, Broad Institute of MIT and Harvard

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 DISCOVAR

:: MORE INFORMATION

Omega 1.0.2 – Overlap-graph de novo Assembler for Metagenomics

Omega 1.0.2

:: DESCRIPTION

Omega is a software for assembling and scaffolding Illumina sequencing data of microbial communities.

::DEVELOPER

the Pan lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Omega

:: MORE INFORMATION

Citation

Omega: an Overlap-graph de novo Assembler for Metagenomics.
Haider B, Ahn TH, Bushnell B, Chai J, Copeland A, Pan C.
Bioinformatics. 2014 Jun 19. pii: btu395.

kronos 2.3.0 – Workflow Assembler for Cancer Genome Analytics and Informatics

kronos 2.3.0

:: DESCRIPTION

Kronos is a software platform for facilitating the development and execution of modular, auditable, and distributable bioinformatics workflows.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Python

:: DOWNLOAD

kronos

:: MORE INFORMATION

Citation

Gigascience. 2017 Jul 1;6(7):1-10. doi: 10.1093/gigascience/gix042.
Kronos: a workflow assembler for genome analytics and informatics.
Taghiyar MJ, Rosner J, Grewal D, Grande BM, Aniba R, Grewal J, Boutros PC, Morin RD, Bashashati A, Shah SP

SLICEMBLER – Meta-assembler Designed for Ultra-deep Sequencing data

SLICEMBLER

:: DESCRIPTION

SLICEMBLER is a meta-assembler designed for ultra-deep sequencing data

:: DEVELOPER

the algorithm and computational biology lab, university of California

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / windows/ MacOsX
  • Python

:: DOWNLOAD

 SLICEMBLER

:: MORE INFORMATION

Citation

De novo meta-assembly of ultra-deep sequencing data.
Mirebrahim H, Close TJ, Lonardi S.
Bioinformatics. 2015 Jun 15;31(12):i9-i16. doi: 10.1093/bioinformatics/btv226.

ALLPATHS-LG 51750 – Whole Genome Shotgun Assembler

ALLPATHS-LG 51750

:: DESCRIPTION

ALLPATHS-LG (Large Genome) is a whole genome shotgun assembler that can generate high quality assemblies from short reads. It works on both small and large (mammalian size) genomes. To use it, you should first generate ~100 base Illumina reads from two libraries: one from ~180 bp fragments, and one from ~3000 bp fragments, both at about 45x coverage. Sequence from longer fragments will enable longer-range continuity.

::DEVELOPER

Computational R&D, The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ALLPATHS-LG

:: MORE INFORMATION

Citation

Gnerre S, MacCallum I, Przybylski D, Ribeiro F, Burton J, Walker B, Sharpe T, Hall G, Shea T, Sykes S, Berlin A, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB. 2010.
High-quality draft assemblies of mammalian genomes from massively parallel sequence data.
Proceedings of the National Academy of Sciences USA (epub ahead of print, Dec. 27, 2010).

PERGA 0.5.03.02 – Paired End Reads Guided Assembler

PERGA 0.5.03.02

:: DESCRIPTION

PERGA is a novel sequence reads guided de novo assembly approach which adopts greedy-like prediction strategy for assembling reads to contigs and scaffolds.

::DEVELOPER

PERGA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PERGA

:: MORE INFORMATION

Citation

PERGA: a paired-end read guided de novo assembler for extending contigs using SVM and look ahead approach.
Zhu X, Leung HC, Chin FY, Yiu SM, Quan G, Liu B, Wang Y.
PLoS One. 2014 Dec 2;9(12):e114253. doi: 10.1371/journal.pone.0114253.