Tag: Assemblies

SKESA 2.4.0 – Strategic K-mer Extension for Scrupulous Assemblies

SKESA 2.4.0

:: DESCRIPTION

SKESA is a de-novo sequence read assembler for microbial genomes. It uses conservative heuristics and is designed to create breaks at repeat regions in the genome.

::DEVELOPER

NCBI – National Center for Biotechnology Information

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SKESA

:: MORE INFORMATION

Citation

Souvorov A, Agarwala R.
SAUTE: sequence assembly using target enrichment.
BMC Bioinformatics. 2021 Jul 21;22(1):375. doi: 10.1186/s12859-021-04174-9. PMID: 34289805; PMCID: PMC8293564.

Souvorov A, Agarwala R, Lipman DJ.
SKESA: strategic k-mer extension for scrupulous assemblies.
Genome Biol. 2018 Oct 4;19(1):153. doi: 10.1186/s13059-018-1540-z. PMID: 30286803; PMCID: PMC6172800.

CrossMap 0.5.3 – Convert Genome Coordinates Between Assemblies

CrossMap 0.5.3

:: DESCRIPTION

CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies.

::DEVELOPER

CrossMap team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Python
  • C++ Compiler

:: DOWNLOAD

  CrossMap

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Apr 1;30(7):1006-7. doi: 10.1093/bioinformatics/btt730. Epub 2013 Dec 18.
CrossMap: a versatile tool for coordinate conversion between genome assemblies.
Zhao H1, Sun Z, Wang J, Huang H, Kocher JP, Wang L.