SAMMate 2.7.4 / assemblySAM 1.1 – Processing Short Read Alignments in SAM/BAM format / RNA-Seq Assembly and Analysis

SAMMate 2.7.4 / assemblySAM 1.1

:: DESCRIPTION

SAMMate is an open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate.

assemblySAM employs a novel method to localize and assemble RNA-seq reads into RNA transcript sequences.

::DEVELOPER

Dongxiao Zhu, Ph.D

:: SCREENSHOTS

sammate

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Java
  • R package

:: DOWNLOAD

 SAMMate / assemblySAM

:: MORE INFORMATION

Citation:

Source Code Biol Med. 2011 Jan 13;6(1):2. doi: 10.1186/1751-0473-6-2.
SAMMate: a GUI tool for processing short read alignments in SAM/BAM format.
Xu G1, Deng N, Zhao Z, Judeh T, Flemington E, Zhu D.

Nguyen, T, Zhao, Z, Zhu, D.
SPATA: A seeding and patching algorithm for hybrid transcriptome assembly.

Nguyen, T, Deng, N, Zhu, D.
SASeq: A selective and adaptive shrinkage approach to detect and quantify active transcripts using RNA-Seq.

TIGER – DNA Sequence Assembly

TIGER

:: DESCRIPTION

Tiger is a novel de novo assembly framework  which adapts to available computing resources by iteratively decomposing the assembly problem into sub-problems.

::DEVELOPER

IMPACT Reach Group (Illinois Microarchitecture Project using Algorithms and Compiler Technology)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 TIGER

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012;13 Suppl 19:S18. doi: 10.1186/1471-2105-13-S19-S18. Epub 2012 Dec 19.
TIGER: tiled iterative genome assembler.
Wu XL1, Heo Y, El Hajj I, Hwu WM, Chen D, Ma J.

ALE 20180904 – Assembly Likelihood Estimator

ALE 20180904

:: DESCRIPTION

ALE is a probabalistic framework for determining the likelihood of an assembly given the data (raw reads) used to assemble it. It allows for the rapid discovery of errors and comparisons between similar assemblies.

::DEVELOPER

Scott Clark@Cornell University Center for Applied Mathematics, Rob Egan@Department of Energy Joint Genome Institute

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX
  • C Compiler
  • Python

:: DOWNLOAD

 ALE

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Feb 15;29(4):435-43. doi: 10.1093/bioinformatics/bts723. Epub 2013 Jan 9.
ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies.
Clark SC, Egan R, Frazier PI, Wang Z.

Rnnotator 3.5.0 – de novo Transcriptome Assembly pipeline from stranded RNA-Seq reads

Rnnotator 3.5.0

:: DESCRIPTION

Rnnotator is an automated software pipeline that generates transcript models by de novo assembly of RNA-Seq data without the need for a reference genome.

::DEVELOPER

Zhong Wang at U.S. Department of Energy Joint Genome Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • BioPerl
  • Blat

:: DOWNLOAD

  Rnnotator

:: MORE INFORMATION

Citation

BMC Genomics. 2010 Nov 24;11:663. doi: 10.1186/1471-2164-11-663.
Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads.
Martin J, Bruno VM, Fang Z, Meng X, Blow M, Zhang T, Sherlock G, Snyder M, Wang Z.

TRUST4 v0.1.1 – TCR and BCR Assembly from RNA-seq data

TRUST4 v0.1.1

:: DESCRIPTION

TRUST (T cell receptor Repertoire Utilities for Solid Tissue/Tumor) is a toolbox for analyzing T cell receptors in solid tumors using unselected RNA-seq data based on de novo assembly.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

TRUST

:: MORE INFORMATION

 

bcm-ace-plots – Reads in an Ace format Assembly File produced by the Phrap

bcm-ace-plots

:: DESCRIPTION

bcm-ace-plots reads in an Ace format assembly file produced by the Phrap (Green et al.) assembly software. Using special tags in the read names, bcm-ace-plots will plot the template coverage, the template span, the coverage, the BAC coverage, the WGS coverage, quality, and high quality discrepancies.

::DEVELOPER

Human Genome Sequencing Center, Baylor College of Medicine

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  MacOsX
  • Java

:: DOWNLOAD

bcm-ace-plots

:: MORE INFORMATION

Kourami v0.9.6 – Graph-guided Assembly for HLA alleles

Kourami v0.9.6

:: DESCRIPTION

Kourami is a graph-guided assembler for HLA haplotypes covering typing exons (exons 2 and 3 for Class I and exon 3 for Class II) using high-coverage whole genome sequencing data.

::DEVELOPER

Kingsford Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs
  • JDK

:: DOWNLOAD

Kourami

:: MORE INFORMATION

Citation

Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery.
Lee H, Kingsford C.
Genome Biol. 2018 Feb 7;19(1):16. doi: 10.1186/s13059-018-1388-2.

FindPlasmids 20180522 – Find plasmids in Microbial Genome Assembly Files

FindPlasmids 20180522

:: DESCRIPTION

FindPlasmids identifies known plasmids in genome assembly files by using the assembly file to query a local Blast+ database of plasmid sequences.

::DEVELOPER

Barry G. Hall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

FindPlasmids

:: MORE INFORMATION

 

LASER – Large genome ASsembly EvaluatoR

LASER

:: DESCRIPTION

LASER is based on QUAST genome assembly program and provides huge performance improvements for large genomes.

::DEVELOPER

LUCIAN ILIE

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

LASER

:: MORE INFORMATION

Citation

LASER: Large genome ASsembly EvaluatoR.
Khiste N, Ilie L.
BMC Res Notes. 2015 Nov 24;8:709. doi: 10.1186/s13104-015-1682-y.

SAGE 2 – String Graph Assembly of GEnomes

SAGE 2

:: DESCRIPTION

SAGE is a new string-overlap graph-based de novo genome assembler.

::DEVELOPER

LUCIAN ILIE

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SAGE

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Sep 15;15:302. doi: 10.1186/1471-2105-15-302.
SAGE: String-overlap Assembly of GEnomes.
Ilie L1, Haider B, Molnar M, Solis-Oba R.