some NGS scripts

http://wiki.bioinformatics.ucdavis.edu/index.php/Data_Analysis

• fastqForensics.pl .. simple report on possible quality encoding formats for a fastq file (Joe Fass)
• count_fasta.pl .. obtain length histogram, GC-content, etc. for sequences in a fasta-format file (Brad Sickler / Joe Fass)
• Nx.pl .. calculate "Nx" stat for a set of sequences in fasta format (Joe Fass)
• fasta1line.pl .. remove newlines to put all sequence on one line following header line, for all sequences in a fasta-format file (Joe Fass)
• fakefastq.pl .. need fastq, and you only have fasta? fake it! {Joe Fass)
• rc.pl .. reverse complement a set of fasta-format sequences (Joe Fass)
• rcFastq.pl .. reverse complement a set of single-line fastq sequences (Joe Fass)
• trim.pl .. trim paired-end fastq files based on quality using a variety of trimming methods (Nikhil Joshi)
• subsequence.pl .. cut out a sub-sequence from sequences and qualities in a fasta/q-format file (Joe Fass)
• SeqQA.pl .. Sequence qualitative analysis for fasta and fastq files (Hans Vasquez-Gross)
• IllQ2SanQ.pl .. Convert Illumina (pipeline 1.3 and above) fastq format to Sanger fastq format (cat sequence.txt | ./IllQ2SanQ.pl > sequence.fastq) (Joe Fass)
• illTrim.pl .. trim Illumina read 3' ends at the first "bad" base .. takes and produces fastq (cat sequence.fastq | ./illTrim.pl > sequence.trimmed.fastq) (Joe Fass)
• trimBWAstyle.pl .. trimming script for oneline fastq, based on Heng Li's clipping algorithm implemented in bwa (for all-bad reads, substitutes one "N") (Joe Fass)
• trim.slidingWindow.pl .. trimming script for oneline fastq, using a sliding window; chucks reads that get trimmed too short (Joe Fass)
• subset_fastq.pl .. get subset of fastq records based on fraction or number of records desired (Nikhil Joshi)
• export2fastq.pl .. convert Illumina's "export.txt" format into fastq (no quality conversion, so equivalent to their "sequence.txt" files) (Joe Fass)
• fastq3pAdapterTrim.pl .. rudimentary 3'-adapter trimming; allows 1-mismatch down to a minimum length of adapter 5'-end (Joe Fass)
• SNPseqRetrieve.pl .. generate SNP sequences in a tab-separated-value format, including flanking sequence from read consensus or reference genome when no reads mapped (Joe Fass)