broadinstitute catch issues

broadinstitute / catch

A package for designing compact and comprehensive capture probe sets.

MIT License

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issues

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Is it possible to design high-throughput DNA probles for plant genomes using CATCH?

#62 ShawnGao911101 opened 1 month ago
3
Decreasing the number of probes outputted

#61 ayesha-mahfuz opened 1 month ago
1
Melting temperature of probes

#60 leocaserta opened 2 months ago
1
usage of pool.py

#59 higx360 opened 4 months ago
1
Option to avoid ambiguous nucleotides in generated probes

#58 med-ss20 opened 5 months ago
1
Expand descriptions of LSH-relevant arguments in README and help messages

#57 haydenm closed 10 months ago
1
Problem install Catch

#56 OrsonMM closed 1 year ago
2
Error running design.py: unexpected keyword argument 'avoided_genomes'

#55 MGeraerts closed 1 year ago
3
Bump scipy from 1.8.0 to 1.10.0

#54 dependabot[bot] opened 1 year ago
0
Switch to GitHub Actions for build testing

#53 haydenm closed 1 year ago
1
Remove viral datasets distributed with CATCH

#52 haydenm closed 1 year ago
0
Add heuristic to decide which clustering method to use

#51 haydenm closed 2 years ago
2
Fix crash on macOS with Python 3.8+

#50 haydenm closed 2 years ago
1
CATCH fails on macOS starting with Python 3.8

#49 haydenm closed 2 years ago
0
Error using design.py

#48 acticu closed 2 years ago
2
Fix bugs in edge cases handling small input

#47 haydenm closed 2 years ago
1
Enhance usability for large, diverse input

#46 haydenm closed 2 years ago
1
Improve hash function in MinHash family

#45 haydenm closed 2 years ago
1
Update Python, NumPy, and SciPy versions to more recent versions

#44 haydenm closed 2 years ago
1
Fix initial guess to be within bounds

#43 haydenm closed 2 years ago
1
Error when running design.py example

#42 FyisFe closed 2 years ago
2
Improve handling of the case when there are no candidate probes

#41 haydenm closed 4 years ago
2
catch on large input

#40 boucherufl closed 4 years ago
4
identify conserved regions or regions suitable for differential identification, and design PCR primer

#39 aiqubo closed 4 years ago
2
Fix --cluster-from-fragments bug with long fragment length

#38 haydenm closed 4 years ago
2
build from clustered segments results in probes w/ less than target coverage

#37 audy closed 4 years ago
3
Add option to save table of the number of sequences each probe maps to

#36 haydenm closed 4 years ago
0
Add option to save table of the number of sequences each probe maps to

#35 haydenm closed 4 years ago
1
Update of dataset all viruses

#34 jhayer closed 4 years ago
1
clarification of -e and -m flag function

#33 EnriqueDoster closed 4 years ago
2
Issue running design.py on large files

#32 EnriqueDoster closed 4 years ago
3
Simplify determination of package version

#31 haydenm closed 5 years ago
1
Update numpy/scipy requirements

#30 haydenm closed 5 years ago
1
Add code of conduct document

#29 haydenm closed 5 years ago
2
Replicability Zika probes Metsky et al Nature Biotechnology

#28 joanmarticarreras closed 5 years ago
3
Add ability to automatically download sequences for a taxonomy

#27 haydenm closed 5 years ago
2
Having trouble accessing preloaded datasets

#26 lkothera closed 5 years ago
12
Add options to cluster input sequences and design on each cluster

#25 haydenm closed 5 years ago
1
Cluster input sequences by producing signatures of them

#24 haydenm closed 5 years ago
1
Allow skipping input sequences that are too short

#23 haydenm closed 5 years ago
1
Add option to filter probes with poly(A) sequence

#22 haydenm closed 5 years ago
1
Speed up construction of universe from IntervalSets

#21 haydenm closed 5 years ago
1
Require -o argument in design.py

#20 haydenm closed 5 years ago
1
Reduce use of ValueError

#19 haydenm closed 5 years ago
1
Error running design.py

#18 jananiharan closed 6 years ago
2
Incorrect fasta paths for some genomes in directories

#17 yesimon closed 6 years ago
1
Expose option to set `kmer_probe_map_k` parameter

#16 haydenm closed 6 years ago
1
Add error message explaining why probe count constraint cannot be satisfied

#15 haydenm closed 6 years ago
1
Expose option to specify a custom hybridization model

#14 haydenm closed 6 years ago
1
Use locality-sensitive hashing to reduce space of candidate probes

#13 haydenm closed 6 years ago
1