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106 Open 156 Closed
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Issues list

explore Tinted De Bruijn graphs for k-mer to read indexing
#516 opened Feb 23, 2024 by ctb
Error in bcalm_catlas_prepare_input
#512 opened Jan 8, 2024 by ccbaumler
1
12
ModuleNotFoundError: No module named 'Cython' error when install sgc on EC2 instance
#511 opened Dec 9, 2023 by jessicalumian
2
Interpretation of first_doms.txt
#508 opened Nov 16, 2023 by alarasutcu
Error in make_contigs_kmer_index: ValueError: max() arg is an empty sequence
#507 opened Oct 25, 2023 by taylorreiter
1
What should we benchmark?
#485 opened Dec 20, 2022 by ccbaumler
1
look into GGCAT for compaction
#470 opened Oct 25, 2022 by ctb
is it time for spacegraphcats v3?
#469 opened Sep 22, 2022 by ctb
1
Snakemake error when building catlas
#467 opened Sep 19, 2022 by christygrettenberger
6
are neighborhoods shell-like?
#465 opened Aug 23, 2022 by ctb
figure out how to extract a subgraph and then run hmm annotation on that subgraph
#464 opened Aug 4, 2022 by taylorreiter
does protein query support degenerative amino acid alphabets?
#463 opened Aug 4, 2022 by taylorreiter
2
can we convert the cDBG to GFA format with the current output files from spacegraphcats?
#462 opened Jul 12, 2022 by taylorreiter
2
spacegraphcats extract_reads as part of larger snakemake workflows: documenting strategies to solve the one:many problem when the many queries are unknown at the beginning of the workflow documentation
#461 opened Jun 2, 2022 by taylorreiter
experiment with AGC for fast retrieval of unitigs
#457 opened Apr 8, 2022 by ctb
1
pruning variation from variation graphs in reference eukaryotic genomes improves accuracy and recall of read alignment: thoughts for application of theory to metapangenome/metaspecies graphs
#456 opened Feb 23, 2022 by taylorreiter
snakemake errors when running sgc
#455 opened Feb 11, 2022 by dnolin13
3
paper: RepBin: Constraint-based Graph Representation Learning for Metagenomic Binning
#453 opened Jan 22, 2022 by ctb
integrate gather-style approach directly into spacegraphcats?
#452 opened Jan 16, 2022 by ctb
7
should we add abundance counting into config file?
#451 opened Dec 6, 2021 by ctb
3
explore bcalm max-memory parameter
#450 opened Nov 27, 2021 by ctb
annotating graphs with proteins, round 2
#448 opened Nov 16, 2021 by ctb
4
get allele seqs (and/or SNPs) from sgc GFA file?
#446 opened Oct 26, 2021 by maureenbug
3
ProtectedOutputException: Write-protected output files for rule bcalm_catlas_prepare_input: GCF_000765235.1_k31/bcalm.unitigs.db
#445 opened Oct 25, 2021 by taylorreiter
5
Documentation of the file headers in the catlas output documentation
#440 opened Oct 6, 2021 by drtamermansour
3
ProTip! Exclude everything labeled bug with -label:bug.