Available Crumbs
- sff_extract
- Extracts reads from an SFF file used by 454 and Ion Torrent.
- split_matepairs
- Splits mate-pairs separated by an oligo sequence.
- filter_by_quality
- Filters sequences according to mean quality.
- filter_by_length
- Filters sequences according to maximum and minimum length thresholds.
- filter_by_name
- Filters sequences with a list of names given in a file.
- filter_by_blast
- Filters the sequences using BLAST.
- filter_by_complexity
- Filters sequences according to their complexity.
- filter_by_bowtie2
- It filters the sequences using bowtie2
- trim_by_case
- Trims sequences according to case.
- trim_edges
- Removes a fixed number of residues from sequence edges.
- trim_quality
- Removes, using a sliding window, regions of low quality in the edges.
- trim_blast_short
- Removes oligonucleotides by using the blast-short algorithm.
- convert_format
- Converts between the different supported sequence formats.
- guess_seq_format
- Guesses the format of a file, including Sanger and Illumina fastq formats.
- cat_seqs
- Concatenates one or several input sequence files, possibly in different formats, into one output.
- seq_head
- Outputs only the first sequences of the given input.
- sample_seqs
- Outputs a random sampling of the input sequences.
- count_seqs
- It counts sequences in the input files
- change_case
- Modifies the case of sequences. Case can be converted to lower or upper, or swapped.
- pair_matcher
- Filters out orphaned read pairs.
- interleave_pairs
- Interleaves two ordered paired read files.
- deinterleave_pairs
- Splits an ordered file of paired reads into two files, one for each end.
- calculate_stats
- Generates basic statistics for the given sequence files.
- orientate_transcripts
- Reverse complements transcripts according to polyA, ORF or BLAST hits.
- fastqual_to_fastq
- Converts fasta and qual files to a fastq format file.