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kallisto_windows-v0.51.1.tar.gz (4.0 MB)
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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| Parent folder | |||
| kallisto_windows-v0.48.0.zip | 2022-01-19 | 3.0 MB | |
| Increase in generalizability of _kallisto bus_.tar.gz | 2022-01-17 | 2.7 MB | |
| Increase in generalizability of _kallisto bus_.zip | 2022-01-17 | 2.9 MB | |
| README.md | 2022-01-17 | 2.3 kB | |
| kallisto_mac-v0.48.0.tar.gz | 2022-01-17 | 1.5 MB | |
| kallisto_linux-v0.48.0.tar.gz | 2022-01-17 | 2.0 MB | |
| Totals: 6 Items | 12.0 MB | 0 | |
New features
- kallisto quant-tcc: This new command can run the EM algorithm on a supplied transcripts-compatibility counts (TCC) matrix file, such as that generated by "bustools count", to generate transcript-level estimates. When a gene-mapping file is supplied, gene-level abundances will also be outputted. Effective length normalization will only be performed if a kallisto index is supplied and if fragment length information is provided.
- New technologies were added to "kallisto bus": -x SmartSeq3 (--tag can be used to supply a 5′ tag sequence that identifies UMI-containing reads), -x BDWTA (BD Rhapsody), -x Visium (10x Visium), -x SPLIT-SEQ (SPLiT-seq preprocessing), and -x Bulk (for preprocessing non-demultiplexed Bulk RNA-seq files)
- "kallisto bus" can be run with no technology specified: In this case, it will either process a batch file (supplied via --batch) like in the old "kallisto pseudo" or will process fastQ files supplied directly on the command line, treating each fastQ file or each pair of fastQ file (if --paired is specified) as an individual sample. This is useful for generating BUS files when each sample is in a separate fastQ file. With bustools and kallisto quant-tcc, this feature effectively entirely deprecates the old "kallisto pseudo".
- Strand-specificity is now enabled by default for 10X, SureCell, CelSeq, BD Rhapsody, and Smart-seq3 UMI technologies (unstranded is default for other technologies) and the user can override this by supplying --fr-stranded, --rf-stranded, and --unstranded options.
- Various performance improvements (mostly in regards to data ingestion throughput)
- A minimal form of the kallisto index is outputted in a file named index.saved and a file containing fragment length distributions (flens.txt) is outputted when "kallisto bus" is run on paired-end reads (which can be specified via the option --paired). This is so kallisto quant-tcc can perform effective length normalization should the need arise.
Deprecation
- "kallisto pseudo" is now deprecated and will be removed in a future release; users should supply batch files of fastQ file names to "kallisto bus" instead
Fixes
- Issue [#319] : <limits> header import
- Issue [#272] : "kallisto quant" and "kallisto pseudo" inconsistency (now fixed)
