useful scripts for genomics
Description:
FastaStats.sh: get statistics on input .fasta file (read length, read name, read number)MapTableFullCigar.sh: get statistics on aligners output given alignment file in .sam format and sequencing read file in .fasta format - used for benchmark of aligners when the aligner is set to output a .sam with full cigar string (aka, reporting details on matches and mismatches information (X,=))MapTable.sh: get statistics on aligners output given alignment file in .sam format and sequencing reads in .fasta format - used for banchmark of aligners when the aligner is set to output a general cigar string, with broad information about alignment match (M)CoverageCalculator.sh: get raw coverage information for uneven read length sequencing data (based on median)