mSWEEP v2.0.0 - Githubissues

PROBIC / mSWEEP

mSWEEP High-resolution sweep metagenomics using fast probabilistic inference

MIT License

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mSWEEP v2.0.0 #23

Closed tmaklin closed 1 year ago

tmaklin commented 1 year ago

First major version increment of mSWEEP (breaks backwards-compatibility).

Output format changes:

Add the total number of reads to the abundances file (resolves #21)
Renamed total_hits to num_aligned in the abundances file (#21)

New features

Added an option to evaluate the mGEMS binning algorithm from the mSWEEP call with the --bin-reads toggle. (https://github.com/PROBIC/mSWEEP/commit/54004d8c2408764dbd970cd1a49c253ede92ce5d)
Support reading alignments compressed with alignment-writer. (https://github.com/PROBIC/mSWEEP/commit/f169fccbf976a0994863e0ffca4a62718778594c)
Read alignments from cin. (https://github.com/PROBIC/mSWEEP/commit/9878f8ef4d342b72877409001e153ffc0433318a)

Removed features:

Matching a fasta file to groups indicators is no longer supported (deprecated options --fasta, --groups-list, --groups-delimiter).

Pseudoaligner support

Removed kallisto support (remove-kallisto-support)
Removed support for Themisto v1.2.0 and older. (remove-kallisto-support)

Installation

Added a conda recipe and instructions on installing mSWEEP from bioconda. (#22)

Build pipeline changes

Removed support for building zlib from source (https://github.com/PROBIC/mSWEEP/commit/5c94591b392932efd7b1d16cb6c3e3ddc688c8e1)
Added the CMAKE_BUILD_WITH_FLTO flag for building with link-time optimization (https://github.com/PROBIC/mSWEEP/commit/ee1db015e9902eca05293a416576e89f1d54af7a)