InDelFixer 1.1 – An Insertion and Deletion Fixing Aligner for 454, Illumina and PacBio

InDelFixer 1.1

:: DESCRIPTION

InDelFixer is a java program to remove frame shift causing insertions or deletions from next-generation sequencing data.

::DEVELOPER

the Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 InDelFixer

:: MORE INFORMATION

ConsensusFixer 0.4 – Consensus Sequence Caller with Ambiguous bases and in-frame Insertions

ConsensusFixer 0.4

:: DESCRIPTION

ConsensusFixer is a java command line application which computes a consensus sequence with in-frame insertions and ambiguous nucleotide (wobbles) from ultra deep next-generation sequencing alignments.

::DEVELOPER

Armin Töpfer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Java

:: DOWNLOAD

 ConsensusFixer

:: MORE INFORMATION

iMembrane – Homology-Based Insertion of Proteins into the Membrane

iMembrane

:: DESCRIPTION

iMembrane is a homology-based method, which predicts a membrane protein’s position within a lipid bilayer. It projects the results of coarse-grained molecular dynamics simulations onto any membrane protein structure or sequence provided by the user.

::DEVELOPER

the Oxford Protein Informatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser
  • Java

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Apr 15;25(8):1086-8. doi: 10.1093/bioinformatics/btp102. Epub 2009 Feb 23.
iMembrane: homology-based membrane-insertion of proteins.
Kelm S, Shi J, Deane CM.

ICC 2.0.1 – Insertion, Deletion and Carry-forward Error Correction for Next-generation Sequencing

ICC 2.0.1

:: DESCRIPTION

ICC (Indel and Carryforward Correction) is a software pipeline to analyze 454 pyrosequencing data, including read quality filtering and alignment, indel and carryforward error correction, single nucleotide variant calling, and calculation of nucleotide variant and hyplotype frequencies.

::DEVELOPER

Mullins Molecular Retrovirology Lab, University of Washington.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

 ICC

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Oct 1;29(19):2402-9. doi: 10.1093/bioinformatics/btt434. Epub 2013 Jul 29.
Indel and Carryforward Correction (ICC): a new analysis approach for processing 454 pyrosequencing data.
Deng W1, Maust BS, Westfall DH, Chen L, Zhao H, Larsen BB, Iyer S, Liu Y, Mullins JI.

iPool-Seq v1.0.3 – Analysis Pipeline for Insertion Pool Sequencing data

iPool-Seq v1.0.3

:: DESCRIPTION

The iPool-Seq analysis pipeline is based on the TRUmiCount algorithm for the quantitative analysis of UMI data, and takes are of all steps of the analysis of iPool-Seq data. From from raw sequencing reads it computes the differential virulences of the mutants in the pre-infection pool compared to a set of reference mutants.

::DEVELOPER

the Center of Integrative Bioinformatics Vienna (CIBIV)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

iPool-Seq

:: MORE INFORMATION

Citation

Insertion Pool Sequencing for Insertional Mutant Analysis in Complex Host-Microbe Interactions.
Uhse S, Pflug FG, von Haeseler A, Djamei A.
Curr Protoc Plant Biol. 2019 Sep;4(3):e20097. doi: 10.1002/cppb.20097.

GINDEL 201601 – Deletion and Insertion Genotype Calling

GINDEL 201601

:: DESCRIPTION

GINDEL is an approach for calling genotypes of both insertions and deletions from sequence reads.

::DEVELOPER

GINDEL team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GINDEL

:: MORE INFORMATION

Citation:

PLoS One. 2014 Nov 25;9(11):e113324. doi: 10.1371/journal.pone.0113324. eCollection 2014.
GINDEL: accurate genotype calling of insertions and deletions from low coverage population sequence reads.
Chu C, Zhang J, Wu Y

Pindel 0.2.5b8 – INDEL (insertions and deletions) Detection

Pindel 0.2.5b8

:: DESCRIPTION

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

::DEVELOPER

The Genome Institute at Washington University School of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 Pindel

:: MORE INFORMATION

Citation:

Bioinformatics. 2009 Nov 1;25(21):2865-71. Epub 2009 Jun 26.
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.
Ye K, Schulz MH, Long Q, Apweiler R, Ning Z.

AgilePindelFilter 20130517 – Identification of Insertions and Deletions as well as large scale Rearrangements using Exome data

AgilePindelFilter 20130517

:: DESCRIPTION

AgilePindelFilter enables the rapid filtering, screening and sorting of indel variants derived from an exome sequencing experiment to allow the rapid detection of possible deleterious variants.

::DEVELOPER

Leeds Institute of Molecular Medicine

:: SCREENSHOTS

AgilePindelFilter

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0

:: DOWNLOAD

 AgilePindelFilter

:: MORE INFORMATION

Citation

Robust diagnostic genetic testing using solution capture enrichment and a novel variant-filtering interface.
Watson CM, Crinnion LA, Morgan JE, Harrison SM, Diggle CP, Adlard J, Lindsay HA, Camm N, Charlton R, Sheridan E, Bonthron DT, Taylor GR, Carr IM.
Hum Mutat. 2014 Apr;35(4):434-41. doi: 10.1002/humu.22490.

MosLocator – Identification of Mos1 Insertions in the C.elegans Genome

MosLocator

:: DESCRIPTION

MosLocator is a tool for researchers who wish to look for insertions in or near one or many genes. It sends queries to a local database; depending on the number of queries and connection speeds, it may take a few seconds or even a couple of minutes for the answer to come back.

::DEVELOPER

the Ewbank lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2012;7(2):e30482. doi: 10.1371/journal.pone.0030482. Epub 2012 Feb 8.
A genome-wide collection of Mos1 transposon insertion mutants for the C. elegans research community.
Vallin E1, Gallagher J, Granger L, Martin E, Belougne J, Maurizio J, Duverger Y, Scaglione S, Borrel C, Cortier E, Abouzid K, Carre-Pierrat M, Gieseler K, Ségalat L, Kuwabara PE, Ewbank JJ.

DDIG-Indel – Detecting DIsease-causing Genetic Variations due to Insertion/Deletion

DDIG-Indel

:: DESCRIPTION

DDIG-Indel (DDIG-in) is a support vector machine-based method to prioritize non-frameshifting indels by comparing disease-associated mutations with putatively neutral mutations from the 1,000 Genomes Project.

::DEVELOPER

Laboratory of Structural Bioinformatics and Design

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

 :: MORE INFORMATION

Citation

Genome Biol. 2013 Mar 13;14(3):R23. [Epub ahead of print] DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels. Zhao H1, Yang Y, Lin H, Zhang X, Mort M, Cooper DN, Liu Y, Zhou Y.