SpacePHARER Release 5-c2e680a

Changes since Release 4-228b9e5:

New features

• Add spacer dataset spacers_dion_et_al_2021 from Dion et al. (2021) in downloaddb

Bugs fixed

• Fix various small memory leaks
• Fix typos
• Fix issue in parsing spacer input in CRT/MinCED format
• Fix issue in handling empty file input
• Fix downloaddb not working when SpacePHARER was called from $PATH instead of a relative or absolute path

SpacePHARER Release 4-228b9e5

Changes since Release 3-5b8c86d:

New features

• Allow restriction of taxonomic resolution based on nucleotide sequence identity (set with --rank-min-seq-ids, turn off by --restrict-rank-mode 0 )
• Add --tax-fdr parameter for host LCA per phage report
• Report possible PAMs also on reverse strand
• Updated base MMseqs2 for additional speedups
• Clean up of command line interface, hide most parameters that are not useful to users

Bugs fixed

• Fix typos
• Fix edge cases in filtermatchbyfdr and restrictranks

SpacePHARER Release 3-5b8c86d

Changes since Release 2-fc5e668:

New features

• Perform additional nucl-nucl alignment on protein-search hits to improve precision (turn off by --perform-nucl-aln 0)
• Add spacer database (Shmakov et al, 2017) to downloaddb
• Report host LCA per phage if mapping file of hosts to taxonomic identifiers is given
• Report phage LCA per spacer if mapping file of phages to taxonomic identifiers is given
• Clean up of command line interface, hide most parameters that are not useful to users
• Updated base MMseqs2 for additional speedups
• SpacePHARER runs on more platforms (x86_64+SSE2, ARM64, PPC64LE)

Breaking changes

• downloadgenome is now called downloaddb

Bugs fixed

• Fix findpam producing inconsistent output between different strands
• Speed up combineprotnuclaln and summarizeresults

SpacePHARER Release 2-fc5e668

SpacePHARER requires a 64-bit system (check with uname -a | grep x86_64) with at least the SSE4.1 instruction set (check by executing cat /proc/cpuinfo | grep sse4_1 on Linux or sysctl -a | grep machdep.cpu.features | grep SSE4.1 on MacOS).

Changes since Release 1-56925d2:

• Using the --fdr parameter would result in an error.

SpacePHARER Release 1-56925d2

SpacePHARER requires a 64-bit system (check with uname -a | grep x86_64) with at least the SSE4.1 instruction set (check by executing cat /proc/cpuinfo | grep sse4_1 on Linux or sysctl -a | grep machdep.cpu.features | grep SSE4.1 on MacOS).