Fastaq
- fastaq-acgtn_only(1) Replace every non acgtnACGTN with an N
- fastaq-add_indels(1) Deletes or inserts bases at given position(s)
- fastaq-caf_to_fastq(1) Converts a CAF file to FASTQ format
- fastaq-capillary_to_pairs(1) Converts file of capillary reads to paired and unpaired files
- fastaq-chunker(1) Splits sequences into equal sized chunks
- fastaq-count_sequences(1) Counts the sequences in input file
- fastaq-deinterleave(1) Splits interleaved paired file into two separate files
- fastaq-enumerate_names(1) Renames sequences in a file, calling them 1,2,3... etc
- fastaq-expand_nucleotides(1) Makes every combination of degenerate nucleotides
- fastaq-fasta_to_fastq(1) Convert FASTA and .qual to FASTQ
- fastaq-filter(1) Filter sequences to get a subset of them
- fastaq-get_ids(1) Get the ID of each sequence
- fastaq-get_seq_flanking_gaps(1) Gets the sequences flanking gaps
- fastaq-interleave(1) Interleaves two files, output is alternating between fwd/rev reads
- fastaq-make_random_contigs(1) Make contigs of random sequence
- fastaq-merge(1) Converts multi sequence file to a single sequence
- fastaq-replace_bases(1) Replaces all occurrences of one letter with another
- fastaq-reverse_complement(1) Reverse complement all sequences
- fastaq-scaffolds_to_contigs(1) Creates a file of contigs from a file of scaffolds
- fastaq-search_for_seq(1) Find all exact matches to a string (and its reverse complement)
- fastaq-sequence_trim(1) Trim exact matches to a given string off the start of every sequence
- fastaq-sort_by_name(1) Sorts sequences in lexographical (name) order
- fastaq-sort_by_size(1) Sorts sequences in length order
- fastaq-split_by_base_count(1) Split multi sequence file into separate files
- fastaq-strip_illumina_suffix(1) Strips /1 or /2 off the end of every read name
- fastaq-to_boulderio(1) Converts to Boulder-IO format, used by primer3
- fastaq-to_fake_qual(1) Make fake quality scores file
- fastaq-to_fasta(1) Converts a variety of input formats to nicely formatted FASTA format
- fastaq-to_mira_xml(1) Create an xml file from a file of reads, for use with Mira assembler
- fastaq-to_orfs_gff(1) Writes a GFF file of open reading frames
- fastaq-to_perfect_reads(1) Make perfect paired reads from reference
- fastaq-to_random_subset(1) Make a random sample of sequences (and optionally mates as well)
- fastaq-to_tiling_bam(1) Make a BAM file of reads uniformly spread across the input reference
- fastaq-to_unique_by_id(1) Remove duplicate sequences, based on their names. Keep longest seqs
- fastaq-translate(1) Translate all sequences in input nucleotide sequences
- fastaq-trim_contigs(1) Trims a set number of bases off the end of every contig
- fastaq-trim_ends(1) Trim fixed number of bases of start and/or end of every sequence
- fastaq-trim_Ns_at_end(1) Trims all Ns at the start/end of all sequences
- fastaq-version(1) Print version number and exit
- fastaq(1) FASTA and FASTQ file manipulation tools