Tag: Indel

SvABA 1.1.0 – Structural Variation and Indel Detection by local Assembly

SvABA 1.1.0

:: DESCRIPTION

SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly.

::DEVELOPER

Jeremiah Wala (jwala@broadinstitute.org) — Rameen Berkoukhim lab — Dana Farber Cancer Institute, Boston, MA.

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SvABA

:: MORE INFORMATION

Citation

Wala JA, Bandopadhayay P, Greenwald NF, O’Rourke R, Sharpe T, Stewart C, Schumacher S, Li Y, Weischenfeldt J, Yao X, Nusbaum C, Campbell P, Getz G, Meyerson M, Zhang CZ, Imielinski M, Beroukhim R.
SvABA: genome-wide detection of structural variants and indels by local assembly.
Genome Res. 2018 Apr;28(4):581-591. doi: 10.1101/gr.221028.117. Epub 2018 Mar 13. PMID: 29535149; PMCID: PMC5880247.

RELINDEL 1.0 – Confidence Score for Indels in Multiple Sequence Alignment

RELINDEL 1.0

:: DESCRIPTION

RELINDEL (RELiable INDELs) is a method to quantify the reliability of indel characters by measuring how often they appear in a set of alternative multiple sequence alignments.

:: DEVELOPER

RELINDEL team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RELINDEL

:: MORE INFORMATION

Citation:

Indel reliability in indel-based phylogenetic inference.
Ashkenazy H, Cohen O, Pupko T, Huchon D.
Genome Biol Evol. 2014 Nov 18;6(12):3199-209. doi: 10.1093/gbe/evu252.

CINDEL – CRISPR AsCpf1 INDEL Score

CINDEL

:: DESCRIPTION

CINDEL is a regression-based model for CRISPR AsCpf1 Indel score, trained with hundreds of in-vitro datasets that Prof. Hyungbum Kim’s lab generated.

:: DEVELOPER

BIG Lab. (BIOINFORMATICS & GENOMICS)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Kim HK, Song M, Lee J, Menon AV, Jung S, Kang YM, Choi JW, Woo E, Koh HC, Nam JW, Kim H.
In vivo high-throughput profiling of CRISPR-Cpf1 activity.
Nat Methods. 2017 Feb;14(2):153-159. doi: 10.1038/nmeth.4104. Epub 2016 Dec 19. PMID: 27992409.

segemehl 0.3 – Fast Short Read Mapping with Indels

segemehl 0.3

:: DESCRIPTION

segemehl is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is able to map primer- or polyadenylation contaminated reads correctly.  segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads gzip‘ed queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping.

::DEVELOPER

the Hoffmann Junior Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  segemehl

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 13. [Epub ahead of print]
Lacking alignments? The next generation sequencing mapper segemehl revisited.
Otto C1, Stadler PF, Hoffmann S.

Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermueller J:
“Fast mapping of short sequences with mismatches, insertions and deletions using index structures“,
PLoS Comput Biol (2009) vol. 5 (9) pp. e1000502

Manta 1.6.0 – Structural Variant and Indel Caller for Mapped Sequencing data

Manta 1.6.0

:: DESCRIPTION

Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads.

::DEVELOPER

Illumina

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 Manta

:: MORE INFORMATION

Citation

Manta: Rapid detection of structural variants and indels for germline and cancer sequencing applications.
Chen X, Schulz-Trieglaff O, Shaw R, Barnes B, Schlesinger F, K?llberg M, Cox AJ, Kruglyak S, Saunders CT.
Bioinformatics. 2015 Dec 8. pii: btv710

UPS-indel – Universal Positioning System of Indels

UPS-indel

:: DESCRIPTION

UPS-indel can be used to compare indels to see whether they are biologically equivalent or not. It can also be used to find out redundant indels.

::DEVELOPER

Professor Zhang Liqing’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 UPS-indel

:: MORE INFORMATION

Citation

Hasan MS, Wu X, Watson LT, Zhang L.
UPS-indel: a Universal Positioning System for Indels.
Sci Rep. 2017 Oct 26;7(1):14106. doi: 10.1038/s41598-017-14400-1. PMID: 29074871; PMCID: PMC5658412.

Vindel 20150218 – A Simple Pipeline for Checking Indel Redundancy

Vindel 20150218

:: DESCRIPTION

Vindel, a simple yet effective computational pipeline, can be used to check whether a given set of indels are redundant with respect to those already in the database of interest such as NCBI’s dbSNP.

::DEVELOPER

Professor Zhang Liqing’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Vindel

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Nov 19;15(1):359. [Epub ahead of print]
Vindel: a simple pipeline for checking indel redundancy.
Li Z, Wu X, He B, Zhang L.

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.

BatAlign – A Short Read Aligner allowing Indels

BatAlign

:: DESCRIPTION

BatAlign is an algorithm that integrated two strategies called ‘Reverse-Alignment’ and ‘Deep-Scan’ to improve the accuracy of read-alignment.

::DEVELOPER

Sung Wing Kin, Ken

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

BatAlign

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2015 Sep 18;43(16):e107. doi: 10.1093/nar/gkv533.
BatAlign: an incremental method for accurate alignment of sequencing reads.
Lim JQ, Tennakoon C, Guan P, Sung WK.

IMSindel – Intermediate-size Indel Detection tool

IMSindel

:: DESCRIPTION

IMSindel is an accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis.

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Ruby

:: DOWNLOAD

IMSindel

:: MORE INFORMATION

Citation

IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis.
Shigemizu D, Miya F, Akiyama S, Okuda S, Boroevich KA, Fujimoto A, Nakagawa H, Ozaki K, Niida S, Kanemura Y, Okamoto N, Saitoh S, Kato M, Yamasaki M, Matsunaga T, Mutai H, Kosaki K, Tsunoda T.
Sci Rep. 2018 Apr 4;8(1):5608. doi: 10.1038/s41598-018-23978-z. Erratum in: Sci Rep. 2018 Jul 4;8(1):10367.