NAME¶
fastaq - FASTA and FASTQ file manipulation tools
SYNOPSIS¶
fastaq <command> [
options]
DESCRIPTION0nf¶
To get minimal usage for a command use: fastaq command
To get full help for a command use one of: fastaq command
-h fastaq
command
--help
Available commands:
acgtn_only Replace every non acgtnACGTN with an N add_indels Deletes or inserts
bases at given position(s) caf_to_fastq Converts a CAF file to FASTQ format
capillary_to_pairs Converts file of capillary reads to paired and unpaired
files chunker Splits sequences into equal sized chunks count_sequences Counts
the sequences in input file deinterleave Splits interleaved paired file into
two separate files enumerate_names Renames sequences in a file, calling them
1,2,3... etc expand_nucleotides Makes every combination of degenerate
nucleotides fasta_to_fastq Convert FASTA and .qual to FASTQ filter Filter
sequences to get a subset of them get_ids Get the ID of each sequence
get_seq_flanking_gaps Gets the sequences flanking gaps interleave Interleaves
two files, output is alternating between fwd/rev reads make_random_contigs
Make contigs of random sequence merge Converts multi sequence file to a single
sequence replace_bases Replaces all occurrences of one letter with another
reverse_complement Reverse complement all sequences scaffolds_to_contigs
Creates a file of contigs from a file of scaffolds search_for_seq Find all
exact matches to a string (and its reverse complement) sequence_trim Trim
exact matches to a given string off the start of every sequence sort_by_size
Sorts sequences in length order split_by_base_count Split multi sequence file
into separate files strip_illumina_suffix Strips
/1 or
/2 off
the end of every read name to_boulderio Converts to Boulder-IO format, used by
primer3 to_fake_qual Make fake quality scores file to_fasta Converts a variety
of input formats to nicely formatted FASTA format to_mira_xml Create an xml
file from a file of reads, for use with Mira assembler to_orfs_gff Writes a
GFF file of open reading frames to_perfect_reads Make perfect paired reads
from reference to_random_subset Make a random sample of sequences (and
optionally mates as well) to_tiling_bam Make a BAM file of reads uniformly
spread across the input reference to_unique_by_id Remove duplicate sequences,
based on their names. Keep longest seqs translate Translate all sequences in
input nucleotide sequences trim_Ns_at_end Trims all Ns at the start/end of all
sequences trim_contigs Trims a set number of bases off the end of every contig
trim_ends Trim fixed number of bases of start and/or end of every sequence
version Print version number and exit