marbl/parsnp
Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
C++NOASSERTION
Issues
- 2
Sequence headers in .xmfa
#31 opened by snayfach - 8
- 1
parsnp.vcf versus parsnp.snps
#25 opened by gotero - 1
- 44
NameError: name 'nameok' is not defined
#51 opened by ramadatta - 0
- 0
Recombination filtering and default parameters
#66 opened by nickp60 - 3
- 2
parsnp run error due to readlinelib
#61 opened by alexadn - 0
parsnp tree node labels
#50 opened by nataliesilmon - 1
Freebayes implementation missing?
#47 opened by sconlan - 3
- 1
parsnp for bins from metagenomic assembly
#37 opened by karchern - 3
Not incorporating all files
#32 opened - 1
no tree calculated
#58 opened by Roman-G1 - 1
issue with gbk file
#22 opened by jfmariet - 1
MUM distance matrix?
#26 opened by gotero - 1
parsnip maf and vcf files
#27 opened by plasmid02 - 1
XMFA file format
#29 opened by sebasso - 1
Parsnp.py input for MUMi
#30 opened by ssmith151 - 6
Failure to install from source
#43 opened by snayfach - 2
- 0
-c option MUMi
#36 opened by nataliesilmon - 2
IndexError: string index out of range
#42 opened by Derreckadam - 1
Order of arguments seems to matter
#44 opened by mjsull - 8
- 8
parsnp cannot find input sequences
#34 opened by ceya - 17
Parsnp error
#49 opened by sambrano - 5
Run error parsnpAligner.ini
#59 opened by innovate-invent - 1
tutorial fails
#60 opened by tbrown99 - 3
libtinfo.so.5: error
#72 opened by Panzenhagen - 1
Over-restrictive file name criteria
#64 opened by innovate-invent - 0
MUMmer not included
#69 opened by bkille - 0
libtinfo.so.5 error
#71 opened by Panzenhagen - 0
Use github submodule for including other tools.
#68 opened by bkille - 1
installation problem
#41 opened by thkuo - 1
How many bootstrap replicates are made for tree reconstruction with Parsnp?
#67 opened by Phytobacteriology-UPNA - 8
Please port to Python3
#63 opened by tillea - 2
Different outputs depending on the file
#65 opened by cfsancas - 4
-l libMUSCLE
#57 opened by tseemann - 7
- 2
Work with 1000 genomes
#48 opened by OrsonMM - 3
configure.ac has wrong parsnp version in it
#55 opened by tseemann - 3
Parsnp 1.2 prints v1.0.1 with parsnp -h
#52 opened by tseemann - 0
- 1
parsnp now in brewsci/bio packaging system
#53 opened by tseemann - 1
Order of genomes in ini file matters?
#46 opened by sconlan - 1
- 1
results: vcf file missing?
#28 opened by karinlag - 1