v0.10.0

Bug fixes:

• Fixes bug where reads were not parsed properly in custom chemistry in which the mappable (biological) sequence spanned more than one read. If one had encountered this bug it would almost certainly be obvious, as you'd likely have seen no mapped reads.

• Fixes bug in paired-end mapping in bulk-mode piscem, when using the poison table, where reads might have wrongly been reported as aligned when they should have been poisoned. This has been fixed and was never present in single-cell-mode, as this is the first release to support biological paired-end single-cell data.

New Features:

• Support for taking advantage of biological paired-end read information, in single-cell data, in protocols supporting this. It is now possible to have "mappable" portions of both read 1 and read 2. These are treated as normal paired-end reads. Currently, for downstream processing of the RAD files, the entire fragment is assigned an orientation (i.e. the orientation of the individual reads are not recorded separately in the RAD file). The current behavior is that for single-end data, the orientation of the mapped read is recorded and for paired-end data, the orientation of the first read in the pair, i.e. read 1, (either observed or implied) is recorded. For example, if a read pair maps with read 1 in the forward orientation and read 2 in the reverse complement orientation, this is recorded as a forward read. Likewise, if read 1 doesn't map but read 2 maps in the reverse complement orientation, this is also considered as a forward read, as reads in paired-end protocols are expected to map in opposite orientations. On the other hand, if the geometry is single-end, and read 2 is the biological read, then the orientation will be recorded as reverse complement if read 2 maps in the reverse complement orientation.

• Explicit flags for chromium_v2_5p, chromium_v3_5p and chromium_v4_3p, corresponding to 10x Chromium v2 and v3 5' chemistries and Chromium v4 3' chemistry respectively.

  • The chromium_v4_3p flag is a convenience, as the geometry is identical to chromium_v3 (though the associated permit list is different), however the distinct flag better conveys intent.

  • The 5' chemistries are treated as biological paired-end protocols by default; that is, if read 1 is long enough to have mappable sequence (i.e. if the length of the read is longer than the barcode length + UMI length + TSO length + k-1, where k is the length of the k-mers used in the piscem index), then that sequence is mapped. However, if read 1 only contains technical information (e.g. UMI and barcode), then just read 2 is mapped. Note however, that treating 5' chemistry as paired-end has implications on the implied orientation reported in the RAD file (see above).

Install piscem 0.10.0

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/piscem/releases/download/v0.10.0/piscem-installer.sh | sh

Download piscem 0.10.0

File	Platform	Checksum
piscem-aarch64-apple-darwin.tar.gz	Apple Silicon macOS	checksum
piscem-x86_64-apple-darwin.tar.gz	Intel macOS	checksum
piscem-x86_64-unknown-linux-gnu.tar.gz	x64 Linux	checksum