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telescope

Convert Themisto pseudoalignments to kallisto pseudoalignments.

Telescope uses the BitMagic library.

Installation

Either use the precompiled binary

or follow the instructions for compiling telescope and libtelescope from source.

Compiling from source

Requirements

  • C++17 compliant compiler.
  • cmake
  • git
  • zlib

How-to

  • Clone the repository, enter the directory and run
> mkdir build
> cd build
> cmake ..
> make
  • This will compile the telescope executable in build/bin/ and the libtelescope library in build/lib/.

Usage

Themisto to kallisto

Convert a single pseudoalignment against 10 reference sequences to kallisto format

telescope --n-refs 10 -r pseudos_1.txt -o kallisto_out_folder

... paired-end reads (pseudoaligned separately) considering a read aligned when either of the reads align

telescope --n-refs 10 -r pseudos_1.txt,pseudos_2.txt -o kallisto_out_folder --mode union

... considering a read aligned when both of the reads align

telescope --n-refs 10 -r pseudos_1.txt,pseudos_2.txt -o kallisto_out_folder --mode intersection

... go crazy and do the same with multiple files (the order of the reads must match for the union and intersection options to make sense)

telescope --n-refs 10 -r pseudos_1.txt,pseudos_2.txt,pseudos_3.txt,pseudos_4.txt -o kallisto_out_folder --mode union

Merge Themisto paired alignment files

Convert two pseudoalignments from paired-end reads to a single pseudos.aln file by intersecting the pseudoalignments

telescope --n-refs 10 -r pseudos_1.txt,pseudos_2.txt -o pseudos --merge

Accepted options

telescope accepts the following flags

-r	Themisto pseudoalignment(s)
-o	Output file directory.
--n-refs	Number of reference sequences in the pseudoalignment.
--merge	Merge the themisto alignments rather than converting to kallisto format (default: false).
--mode	How to merge paired-end alignments (one of union, intersection; default: intersection)
--write-compact	Write themisto format alignments in alignment-writer compressed format (default: true).
--cin	Read the last alignment file from cin (default: false).
--silent	Suppress status messages (default: false)
--help	Print the help message.

License

telescope is licensed under the GNU Lesser General Public License v2.1.

Dependencies

BitMagic is licensed under the Apache-2.0 license.