Contains miscellaneous scripts for genomics

• FASTQtoFASTA.pl - Converts FASTQ files to FASTA/QUAL files. Autodetects Sanger/illumina encoding

• get_SRA.pl - Downloads SRA files from the NCBI FTP site

• orientRNAs - Reorient RNAs in a multifasta file according to their top blast hits

• removeTP.pl - Removes NexteraXT transposon sequences from FASTQ files

• SeqIO.pl - Interconverts common formats. Based on BioPerl's SeqIO module. Requires local installation of BioPerl

• splitMultifasta - Splits a multifasta file into separate fasta (*.fsa) files

• sort_by_coverage.pl - Filters the Contigs.tsv file generated by Ray according to the desired coverage range and minimum length