Ea-Utils

• determine-phred(1) ea-utils: read sam, fastq or pileup and return the phred-scale
• ea-alc(1) ea-utils: Approximate line counts for each file.
• fastq-clipper(1) ea-utils: removes one or more adapter sequences from the fastq file
• fastq-join(1) ea-utils: join two paired-end reads on the overlapping ends
• fastq-mcf(1) ea-utils: detect levels of adapter presence, compute likelihoods and locations of the adapters
• fastq-multx(1) ea-utils: replace % with the barcode id in the barcodes file
• fastq-stats(1) ea-utils: produce lots of easily digested statistics
• fastx-graph(1) ea-utils: R script to process fastq-stats output
• randomFQ(1) ea-utils: return random entries from the input fastq
• sam-stats(1) ea-utils: produce digested statistics
• varcall(1) ea-utils: output summry stats or perform variant calling