Tag: Adjacency

PhySca – SCJ small parsimony problem for weighted Gene Adjacencies

PhySca

:: DESCRIPTION

PhySca samples solutions to the Single-Cut-and-Join (SCJ) small parsimony problem for weighted gene adjacencies.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

PhySca

:: MORE INFORMATION

Citation

Luhmann N, Lafond M, Thevenin A, Ouangraoua A, Wittler R, Chauve C.
The SCJ Small Parsimony Problem for Weighted Gene Adjacencies.
IEEE/ACM Trans Comput Biol Bioinform. 2019 Jul-Aug;16(4):1364-1373. doi: 10.1109/TCBB.2017.2661761. Epub 2017 Jan 31. PMID: 28166504.

NAIBR – Novel Adjacency Identification with Barcoded Reads

NAIBR

:: DESCRIPTION

NAIBR is a probabilistic algorithm for the identification of novel adjacencies from whole-genome linked-read sequencing data. NAIBR takes as input a barcoded and phased BAM processed with 10X Genomics’ “Long Ranger” pipeline and outputs a BEDPE file containing the predicted novel adjacencies with corresponding haplotypes, and log-likelihood scores.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

NAIBR

:: MORE INFORMATION

Citation:

Elyanow R, Wu HT, Raphael BJ.
Identifying structural variants using linked-read sequencing data.
Bioinformatics. 2018 Jan 15;34(2):353-360. doi: 10.1093/bioinformatics/btx712. PMID: 29112732; PMCID: PMC5860216.

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