Bioinformatics at COMAV

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.
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