This repository has been archived as of 20 August 2024 and is no longer maintained.
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.