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.

COSMID – CRISPR Search with Mismatches, Insertions and/or Deletions

COSMID

:: DESCRIPTION

COSMID (CRISPR Off-target Sites with Mismatches, Insertions, and Deletions) is a web-based tool that searches genomes for potential off-target sites (http://crispr.bme.gatech.edu).

::DEVELOPER

Peng Qiu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Cradick TJ, Qiu P, Lee CM, Fine EJ, Bao G.
COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites.
Mol Ther Nucleic Acids. 2014 Dec 2;3(12):e214. doi: 10.1038/mtna.2014.64. PMID: 25462530; PMCID: PMC4272406.

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

:: 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.

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

:: 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