AntonelliLab seqcap_processor issues

AntonelliLab / seqcap_processor

Bioinformatic pipeline for processing Sequence Capture data for Phylogenetics

MIT License

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issues

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IndexError in "reference_assembly" (secapr v 2.2.8)

#40 kroeve closed 3 months ago
1
locus_selection

#39 pabijanM opened 5 months ago
2
--min-coverage in find_target_contigs

#38 pabijanM opened 9 months ago
1
avoid crash when no contigs found by find_target_contigs.py

#37 bmichanderson closed 1 year ago
1
Example file format for secapr clean_reads

#36 nbat64 closed 1 year ago
5
Problem with loci alignments

#35 PierreHenriFabre opened 1 year ago
5
Correct previous correction for int as fasta ref id

#34 bmichanderson closed 2 years ago
0
Correct previous patch for numpy.int64 values as fasta sequence names

#33 bmichanderson closed 2 years ago
1
Fix paralogs_to_ref.py

#32 bmichanderson closed 2 years ago
1
Change parallel processing for assemble_reads.py

#31 bmichanderson closed 2 years ago
1
Adjust parallel processing for assemble_reads.py

#30 bmichanderson closed 2 years ago
2
Fix paralogs_to_ref.py

#29 bmichanderson closed 2 years ago
1
IndexError in "reference_assembly"

#28 kq1986 closed 2 years ago
1
FileExistsError: [Errno 17] File exists: '/home/gmeng/work/4.assembly/secapr/April-5-2022/stats'

#27 linzhi2013 opened 2 years ago
0
ValueError: No objects to concatenate

#26 linzhi2013 opened 2 years ago
0
Paralogs_to_ref

#25 EdBiff opened 2 years ago
0
GC overhead limit exceeded

#24 MikeSanJose opened 2 years ago
2
Division by zero error on aDNA dataset

#23 ThibauldMichel opened 3 years ago
0
KeyError in locus_selection.py

#22 ThibauldMichel opened 3 years ago
0
"Average_cov_per_locus" file missing, causing error in plotting matrices of selected loci?

#21 wtesto closed 3 years ago
1
--disable_stats missing?

#20 BenKuhnhaeuser opened 3 years ago
4
Python 2.7 is end-of-life

#19 marcelm closed 4 years ago
1
problem with find_target_contigs with subset of loci getting dropped wrongly

#18 kvpmulder closed 4 years ago
0
Good loci lost during phasing

#17 brunoasm opened 4 years ago
0
Error with add_missing_sequences

#16 brunoasm opened 4 years ago
0
paralogs_to_ref IndexError

#15 emmawahl closed 4 years ago
1
phase_alleles requires --reference flag parameter

#14 btsinn closed 5 years ago
4
Assembly_reads fails with IOError

#13 ClaudiaPaetzold closed 5 years ago
9
Bug in alignment of phased sequences

#12 brunoasm closed 5 years ago
3
Speeding up find_target_contigs using parallelLastz

#11 RandolphQuek opened 6 years ago
0
Arguments in assemble_reads.py

#10 SergioB1983 closed 5 years ago
2
Reconstructing phased sequences for homozygous individuals

#9 Anh-Thu-Weber closed 4 years ago
1
Removing CLC from mapper possibility

#8 Estel-Kitsune closed 7 years ago
0
Fixing a few typos

#7 Estel-Kitsune closed 7 years ago
0
Recipe fixes

#6 marcelm closed 7 years ago
1
Conda

#5 Estel-Kitsune closed 7 years ago
1
added index file for phased bam files

#4 tandermann closed 8 years ago
0
added bwa mapper to phasing script

#3 tandermann closed 8 years ago
0
Shebang now working on Albiorix 4.0

#2 mtop closed 5 years ago
0
Argument "read_min" in clean_reads.py

#1 Estel-Kitsune closed 8 years ago
1