Convert Themisto pseudoalignments to kallisto pseudoalignments.
Telescope uses the BitMagic library.
Either use the precompiled binary
or follow the instructions for compiling telescope and libtelescope from source.
- C++17 compliant compiler.
- cmake
- git
- zlib
- 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/.
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
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
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.
telescope is licensed under the GNU Lesser General Public License v2.1.
BitMagic is licensed under the Apache-2.0 license.