Back to sequences

Given a set $K$ of kmers (fasta / fastq [.gz] format) and a set of sequences (fasta / fastq [.gz] format), this tool will extract the sequences containing some of those kmers.

A minimal ($m$) and a maximal ($M$) thresholds are proposed. A sequence whose percentage of kmers shared with $K$ are in $]m, M]$ is output with its original header + the number of shared kmers + the ratio of shared kmers:

>original_header 20 6.13
TGGATAAAAAGGCTGACGAAAGGTCTAGCTAAAATTGTCAGGTGCTCTCAGATAAAGCAGTAAGCGAGTTGGTGTTCGCTGAGCGTCGACTAGGCAACGTTAAAGCTATTTTAGGC...

In this case 20 kmers are shared with the indexed kmers. This represents 6.13% of the kmers in the sequence.

Simplest usage

back_to_sequences --in-kmers 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 from 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.

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

Documentation

Full documentation is available at https://b2s-doc.readthedocs.io/en/latest/