Shaun Jackman
Shaun Jackman
It appears to have worked! I see `BX:Z` tags in the alignments, but I don't see any `MI:i` tags. Is there an option to enable `MI:i` tags? > EMA outputs...
No worries, Ariya. Here's the first alignment. ``` @PG ID:ema PN:ema VN:0.6.1 CL:ema align -t16 -r foo.fa -1 /dev/stdin … HISEQX5:19:HYN5VCCXX:4:2223:19664:49338_GCAGTTACAGGTCTGC 99 contig_1 1 0 55S73M = 111 192 ATGTGCTCGCAAGAGTTGGAATGAAACCGGTTGTATTTCCAATGCCTTTATAACTCTCTCTCTAGGTGTAAATATAGGTGCAGAACCTACGGAGTCCCCAGCAGTTCCAGGTGAAGTTTATCCAGACG...
I implemented this feature using `gfapy`. You can close this issue, unless you'd also like to implement it in `gfak`. See https://github.com/ggonnella/gfapy/pull/8
I’d suggest a command `gfak subgraph` that can apply various filtering options specified at the command line, like `-l` for minimum segment length, or `--segment` to specify a list of...
``` Usage: gfaview [options] Options: General: -v INT verbose level [2] -1 only output CIGAR-M operators (for compatibility) -u generate unitig graph (unambiguous merge) Subgraph: -s EXPR list of segment...
``` ❯❯❯ Bandage reduce ⏎ merge ◼ Bandage reduce takes an input graph and saves a reduced subgraph using the graph scope settings. The saved graph will be in GFA...
Both tools allow select a radius of nodes around specified seeds, `gfaview -S` and `Bandage reduce --distance`. Setting that threshold to a large values implements the feature of selecting components...
Thanks, Eric!
I've updated the `gfakluge` Homebrew formula in Brewsci/bio: https://github.com/brewsci/homebrew-bio/pull/366