Protocols

PASHA specifications

Information


Unique identifier OMICS_00024
Name PASHA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Yongchao Liu

Publication for PASHA

PASHA citation

call_split

Palindromic Genes in the Linear Mitochondrial Genome of the Nonphotosynthetic Green Alga Polytomella magna

2013
Genome Biol Evol
PMCID: 3787674
PMID: 23940100
DOI: 10.1093/gbe/evt122
call_split See protocol

[…] SA), using total DNA, isolated with the DNeasy Plant Mini Kit (Qiagen, MD, USA). The P. magna sequence data (∼5 Gb) were assembled de novo with Ray v1.2.1 (), using a k-mer of 21, and separately with PASHA (), using a k-mer of 31. The resulting Ray- and PASHA-generated contigs were independently scanned for mitochondrial sequences using BLAST and the P. capuana and P. parva mtDNAs as search querie […]

PASHA institution(s)
School of Computer Engineering, Nanyang Technological University, Singapore; Institut für Informatik, Johannes Gutenberg University Mainz, Germany

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