📦 fastaq

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• fastaq(1)FASTA and FASTQ file manipulation tools✨
• 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✨