Tag: Error-prone Read

Longshot v0.43 – Diploid SNV Caller for Error-prone Reads

Longshot v0.43

:: DESCRIPTION

Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). It takes as input an aligned BAM file and outputs a phased VCF file with variants and haplotype information. It can also genotype and phase input VCF files. It can output haplotype-separated BAM files that can be used for downstream analysis.

::DEVELOPER

Bansal Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Longshot

:: MORE INFORMATION

Citation

Edge P, Bansal V.
Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing.
Nat Commun. 2019 Oct 11;10(1):4660. doi: 10.1038/s41467-019-12493-y. PMID: 31604920; PMCID: PMC6788989.

FragGeneScan 1.31 – Predicting Genes in Short and Error-prone Reads

FragGeneScan 1.31

:: DESCRIPTION

FragGeneScan is an application for finding (fragmented) genes in short reads.The software combines sequencing error models and codon usages in a hidden Markov model to improve the prediction of protein-coding region in short reads.

::DEVELOPER

Yuzhen Ye lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  FragGeneScan

:: MORE INFORMATION

Citation:

Mina Rho, Haixu Tang, and Yuzhen Ye.
FragGeneScan: Predicting Genes in Short and Error-prone Reads.
Nucl. Acids Res., 2010 doi: 10.1093/nar/gkq747