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
Reference Sequence SNP Call
#118 opened by hdesale2408 - 7
Parsnp tree file does not have distances
#121 opened by Brahmandam-Gayatri - 1
Some nodes have a bootstrap value of zero; what does it mean? Can I increase number of bootstrap replicates?
#131 opened by Phytobacteriology-UPNA - 1
VCF file does not contain indel information
#137 opened by Archaea810 - 1
enhancement : option to fix seed
#138 opened by evezeyl - 1
multi-MUM search and libMUSCLE aligner not working
#136 opened by Despot43 - 13
- 1
Time for converting from .ggr to <multi-fasta alignment output (concatenated LCBs)>
#105 opened by valery-shap - 20
Parsnp command is not working
#123 opened by smruti241 - 5
-x option issue
#108 opened by pasdidee - 3
in <module> if hdr[0] != ">": IndexError: string index out of range error in 1.7.2 release
#114 opened by mf116 - 1
Parsnp skips genome without aligning all
#122 opened by emmannaemeka - 1
Feature Request: use pre-computed alignment
#130 opened by chrisgulvik - 6
Creating empty mblocks file
#124 opened by lkavan2 - 4
No option to use ANI?
#125 opened by nicolettacommins - 2
cpu//threads number :: avoid oversubscription
#120 opened by EricDeveaud - 2
does parsnp use -gtr from fasttree2 by default... or the fasttree2 default, which is jukes-cantor?
#119 opened by Phylloxera - 4
- 2
- 0
- 10
Bootstrap values are not showing up in the tree
#103 opened by naomiohta - 6
Different number of SNPs from same data when ParSNP run on different computers
#99 opened by SarahNadeau - 2
Option to skip tree building
#107 opened by hkaspersen - 2
Fail to force inclusion of all genomes
#104 opened by zjshi - 2
- 1
Allowed symbols in fasta files
#101 opened by valery-shap - 3
issue with parsnp/1.5.4
#91 opened by lanorvege - 8
The following command failed: >>$ /var/miniconda3/envs/parsnp/bin/bin/parsnp_core
#100 opened by bakersjc - 5
AttributeError version 1.5.6
#97 opened by kristij249 - 3
genomes in directory not used?
#96 opened by maguileraf - 1
- 2
AcrB mutation in S. Typhi
#93 opened by fahadkhokhar - 1
- 2
No vcf is generated
#94 opened by empiricalbayes - 7
Failing at raxml step
#88 opened by BioMinnie - 2
- 7
Error command harvest failed
#89 opened by valeriaR89 - 5
Error:ref seq seems to be aligned
#84 opened by tadediran - 3
error : CRITICAL - Profile not in system path!
#86 opened by aliciacb - 2
name 'chr_spos' is not defined in parsnp
#87 opened by ruchi19flowchart - 5
error happens when using sample data to test this
#85 opened by zerodel - 1
Build binary release on older glibc?
#77 opened by tseemann - 21
Remove +/-30% filter
#80 opened by jellila - 1
Parsnp memory issue
#82 opened by bkille - 19
- 12
Not able to detect the target genomes to run
#79 opened by Nits11 - 0
Missing description
#75 opened by tseemann - 4
libMUSCLE make returns error 2
#76 opened by tseemann - 1
setup.py still has version=1.0 in it
#78 opened by tseemann - 1
Cannot open reference file !
#73 opened by lanlan0210