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singularity-builds/assembly_improvement/README.md

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Assembly Improvement

Container source assembly_improvement source Version 1.160490 Docs CentOS base

Take in an assembly in FASTA format, reads in FASTQ format, and make the assembly better by scaffolding and gap filling.

Tools installed

SSPACE

  • SSPACE_Basic.pl

GapFiller

  • GapFiller

Abacas

  • abacas.pl

SGA

  • sga

improve_assembly

  • improve_assembly
  • diginorm_with_khmer
  • fill_gaps_with_gapfiller
  • order_contigs_with_abacas
  • read_correction_with_sga
  • scaffold_with_sspace