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C++ code to evaluate basic stats for a fasta/fastq(.gz) file

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n50

C++ code to evaluate basic stats for a fasta/fastq(.gz) file

Usage: ./n50 <reads.fastq/fasta(.gz)>

Requirements:

  • zlib
  • tested with gcc 4.9.2

To compile:

  • ./install.sh

Output:

  • Bases: total number of bases found in the file
  • contigs: total number of contigs/scaffolds/reads found
  • mean_length: mean lenght of contigs/scaffolds/reads
  • longest: longest contig/scaffold/read
  • N50: contig/scaffold/read N50
  • n: number of contigs/scaffolds/reads contributing to the N50

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C++ code to evaluate basic stats for a fasta/fastq(.gz) file

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