Some basical use cases of back to sequences

Basic case

back_to_sequences --in-kmers compacted_kmers.fasta --in-sequences reads.fasta --out-sequences filtered_reads.fasta  --out-kmers counted_kmers.txt

The filtered_reads.fasta file contains the original sequences (here reads) from reads.fasta that contain at least one of the kmers in compacted_kmers.fasta. The headers of each read is the same as in reads.fasta, plus the estimated ratio of shared kmers and number of shared kmers.

If the --out-kmers option is used, the file counted_kmers.txt contains for each kmer in compacted_kmers.fasta the number of times it was found in filtered_reads.fasta.

Using filters

back_to_sequences --in-kmers compacted_kmers.fasta --in-sequences reads.fasta --out-sequences filtered_reads.fasta  --out-kmers counted_kmers.txt --min-threshold 50 --max-threshold 70

In this case only sequeces from reads.fasta that have more than 50% and at most 70% of their kmers in compacted_kmers.fasta are output.

Specifying strands

back_to_sequences --in-kmers compacted_kmers.fasta --in-sequences reads.fasta --out-sequences filtered_reads.fasta --stranded

In this case, the kmers found in compacted_kmers.fasta are indexed in their original orientation, and kmers extracted from reads.fasta are queried in their original orientation.

Note

Without the --stranded option, all kmers (indexed and queried) are considered in their canonical form.

One may be interested in finding kmers from the reverse complement of the queried sequences. In this case we add the --query-reverse option together with the --stranded option:

back_to_sequences --in-kmers compacted_kmers.fasta --in-sequences reads.fasta --out-sequences filtered_reads.fasta --stranded

Reading sequences from standard input

cat reads.fasta | back_to_sequences --in-kmers compacted_kmers.fasta --out-sequences filtered_reads.fasta

Note

When reading sequences from standard input, do not provide the --in-sequences

Using several input read sets

Say you have three input read files 1.fa, 2.fa, 3.fa to which you wish to apply back_to_sequences.

create an input and an output files:

run back_to_sequences

Output matching kmers

Output the list of matching kmers with their number of occurrences

back_to_sequences enables to output for each kmers in in-kmers set, its number of occurrences in the queried sequences.

In this case the out_kmers.txt file contains, for each kmer from kmer.fa its number of occurrences in the sequence.fa file (canonical or not, depending on the usage of the --stranded option).

Output the list of matching kmers with their position in sequences

back_to_sequences enables to output for each kmers in in-kmers set, its positions in the queried sequences.

In this case the out_kmers.txt file contains, for each kmer from kmer.fa its occurrences in the sequence.fa file. An occurrence is given by a triplet (sequence_id, position, strand). * sequence_id: id (starting from 0) of the sequence from sequence.fa where the kmer occurs. * position: position (starting from 0) where the kmer occurs on the sequence * strand: orientation of the canonical version of the queried kmer in the sequence. This is a bit misleading:

without the stranded option, the position of the canonical version of the kmer is given. This version can be found in the same direction (true) or in the reverse complement direction (false).

with the ‘stranded’ option, the position of the requested version of the kmer is given. Only the forward version of this kmer is found.

Output for each queried sequence its location and strand of shared kmers

back_to_sequences enables to output for each queried sequence, the location and strand of its kmers shared with the in-kmers set.

In this case the out_sequences.fa contains for each queried sequence its usual header (original header number and ratio of shared kmers with the in-kmers set) and additionaly, it shows the location (0-based) of shared kmers. For each location (including 0), the strand is indicated by nothing or a - character if the --stranded option is given.