Changes from v0.42.5

quant mode:

Quantification can now be run in strand specific mode. The experiment can either be --fr-stranded, when the first read is on the forward strand or --rf-stranded
kallisto_mac-v0.43.0.tar.gz
when the first read is on the second strand.

pseudo mode:

• Improved multithreading when working with single cell data.
• A new UMI mode has been added which allows for efficient processing of UMI labelled single cell data.
• Sparse output for batch mode.

pseudo mode:

A new mode kallisto pseudo has been implemented which allows reads to only be pseudoaligned. This mode is useful during single cell analysis as many different experiments (single cells) can be analyzed at the same time and their equivalence classes will be consistent. It will also output a matrix of equivalence class counts (as used in Fast and accurate single-cell RNA-Seq analysis by clustering of transcript-compatibility counts).

Bug fixes:

• Fixes a segfault that could occur when running quant in --bias mode
• Fixes a small error in allocation of memory
• Ensures that single-end reads have reasonable length mappings when mapping to short transcripts

• multithreaded pseudoalignment
• bias parameters and fragment length distribution integrated into HDF5 (integration now exists in sleuth)
• bug fix when read maps to the end of a transcript

• We now use a conditional mean for effective length estimation (rather than the overall mean) based on the frag length distribution
• Add 'aux/num_processed' to H5
• Add GFA file option to 'inspect'
• Incorporate truncated gaussian in single-end datasets instead of only mean

A few bugfixes to v0.42.2 are included here:

• Off-by-one error fix in pseudobam output for reads mapping to reverse strand
• Rare segfault fix happening on Ubuntu 12.02
• -nan values would sometimes show up in abundances in edge case

It is recommended that users upgrade to this release.

This is version 0.42.2 of Kallisto.

Updates include

• index
  • the index has been updated to include more of the transcript information
  • indices should be slightly smaller than before
  • indices constructed with previous versions will not work with this version, rerun your index command
• quant
  • Bootstraps can be run in multithreaded mode, use option -t to specify number of threads
  • If only one read of a paired end maps, kallisto will check the transcript positions to discard reads that would go outside of transcript given the mean fragment length.
  • Pseudobam. Pseudoalignments can now be output in SAM format to standard output. For more details on the output see pseudobam
  • Sequence specific bias. kallisto can learn a model for sequence specific bias and correct the abundances accordingly.
  • TSV. All output text files have been changed to .tsv ending.

This is version 0.42.1 of Kallisto. We recommend that users upgrade to this version.

Updates include

• index
  • now accepts multiple FASTA files and creates an index of all the targets
  • transcripts that end with polyA, runs of length 10 or greater have the polyA tail clipped
• quant
  • now accepts multiple FASTQ paired end files, or single-end files
  • --single flag to specify single-end reads
  • simplified jumping rules
  • uses soft-intersect, if one read has no mapping k-mers the other end is used for pseudoalignment

First public release of kallisto.