mossmatters HybPiper issues

mossmatters / HybPiper

Recovering genes from targeted sequence capture data

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issues

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hybpiper assemble runs but SPAdes assemblies are only made for 1 gene

#158 mheeney opened 1 week ago
1
drop in recovered genes going from 2.1.8 to 2.2.0

#157 HaydenRJones closed 1 week ago
0
hybpiper fix_targetfile

#156 oliviermaurin opened 2 weeks ago
2
HybPiper 2.2.0 Retrieve Sequences and Paralog Retriever failing to run on MacOS

#155 plitof1 opened 3 weeks ago
2
Issues installing - TypeError: main() missing 1 required positional argument: 'args'

#153 ksanb closed 1 month ago
2
Question about .blastx files

#151 wojahn closed 2 months ago
2
Tutorial Heat Map

#149 Gabriel-P-Johnson closed 2 months ago
8
Can't install HybPiper - Getting LibMambaUnsatisfiableError:

#148 plitof1 closed 3 months ago
1
Depreciation of Bio.Application

#147 mossmatters opened 3 months ago
1
--run_intronerate

#146 PiraMew closed 4 months ago
1
Can I assemble chloroplast genes with Hybpiper?

#145 Wyclif3 opened 4 months ago
2
'hybpiper assemble' didn't capture any target genes

#144 xueqinerer opened 4 months ago
3
Issue with paralog_retriever

#143 TiagoVieiraBotany opened 5 months ago
7
Hybpiper2 fails at exonerate

#142 laeserman closed 4 months ago
5
Lower recovery rate using Hybpiper v.2.1.6 compared to v.1.3.1

#141 bingli8899 opened 5 months ago
5
Warning more than one Exonerate hit

#140 pablomurod closed 5 months ago
2
Hybpiper accusing incorrectly formatted fasta headers

#139 TiagoVieiraBotany closed 6 months ago
3
Pipeline stops at distribute_reads_to_targets

#138 paigethebotanist closed 6 months ago
3
Target file - Hybpiper assemble with Spades

#137 perezii opened 7 months ago
0
hybpiper assemble only BWA accomplished, but spades may not be performed

#136 DL-Lin opened 9 months ago
8
procedure always stops halfway

#135 Sourirewang closed 7 months ago
4
Issue with paralog_retriever

#134 erika-r-moore closed 9 months ago
2
Hybpiper not available from installed channels

#133 wtesto closed 11 months ago
2
Issue with retrieve_sequences.py

#132 ZhiqiongMo opened 11 months ago
0
point to bioconda and biocontainer

#131 TomHarrop opened 11 months ago
1
HybPiper on Galaxy

#130 TomHarrop opened 11 months ago
1
Lower Intron Recovery by HybPiper v2.0?

#129 ZhiqiongMo closed 11 months ago
2
Hybpiper Stats

#128 vicmmer closed 4 months ago
5
Issue with distribute_reads_to_targets.py

#127 Kedraous opened 1 year ago
4
exonerate_contigs issue and less genes with seqs in v2.1.5?

#126 joyceem closed 4 months ago
5
Quotation marks in target file gene names results in error

#125 chrisjackson-pellicle closed 2 months ago
1
should --run_intronerate be on by default?

#124 mossmatters closed 4 months ago
4
Overflow error in gene_recovery_heatmap

#123 mossmatters closed 1 year ago
12
Much lower recovery from HybPiper 2.1 than 1.3

#122 V-Z closed 1 year ago
14
Exonerate multiprocessing timeout error

#121 mossmatters closed 2 months ago
1
option in Hybpiper 1.3 not in Hybpiper 2.1

#120 veronicamb opened 1 year ago
14
Question about the --timeout flag

#119 Eremus007 closed 1 year ago
1
Issues installing hybpiper

#118 veronicamb closed 1 year ago
2
fasta headers don't have gene name

#117 GavSmy opened 1 year ago
2
Adding to bioconda

#116 TomHarrop closed 1 year ago
5
Using fix_targetfile messes up with the target file

#115 josh3397 opened 1 year ago
3
Selection of the 'best' target file reference seqeuence for each gene

#114 chrisjackson-pellicle opened 1 year ago
0
Error with running bbmap.sh during the stitched-contig chimera test for some genes.

#113 Oulo opened 1 year ago
5
Output check of contig orientation and reading frame

#112 bmichanderson opened 1 year ago
0
Flag/Subparser to specify output path suggestion

#111 Eremus007 opened 1 year ago
0
exonerate() raised: [Errno 24] Too many open files

#110 Alicia-Talavera opened 1 year ago
11
Spades assembly failes on test-dataset and real dataset

#109 ClaudiaPaetzold closed 1 year ago
2
Title：assemble.py - hybpiper.assemble - assemble - ERROR - ERROR: No genes with reads, exiting!

#108 wang-CK2 closed 1 year ago
5
check_dependencies error

#107 dianzhiyong closed 1 year ago
1
Stop codons in the final assembly

#106 junchen-deng opened 1 year ago
8