Wychung/meeting1130

From CCGB

tool for first step of metagenomics analysis

input

• -method [Solexa, 454, Sanger]
• -seqfile [sequence file name]
• -scorefile [quality score file name]
• -trim [threshold of minumal quality score]
• -length [threshold of minumal read length after trimming]
  • 0 shows the longest substring
• -outfile [sequence output file]

output

• trimmed sequence in fasta format, one file
  • return multiple sequences if same length
• a text file with R code:
  • score distribution --> boxplot
  • length histogram --> before and after trim (longest substring)