Shaun Jackman
Shaun Jackman
Does EMA support mapping reads in the Longranger basic FASTQ format, where the corrected barcode is in the BX:Z tag of the FASTQ header? ``` @E00316:145:HMVG3CCXX:5:1214:6786:3014 BX:Z:AAACACCAGACAATAC-1 ``` Does EMA...
Running `ema` prints the version and `ema help` prints the help message. The customary options are named `ema --version` and `ema --help`.
`gfak extract` outputs blank lines. For example: ``` >7 CTCTTTTTTATTATAATGAAATTTGATTAGTAATAATTCTATTTTATTGTATTAAAAAACAAACTAC >8 GGGTTTATTTGATCAATTTTTGCAATCAATTTCTTGAAACCG >9 AGTATTGAATAAATACTATTTTGAATTAAAGAA ``` There are typically no blank lines in a FASTA file.
I'd like to compact the assembly graph (merge all possible segments). Bandage has this feature from the GUI, but doesn't expose it to the command line. See https://github.com/rrwick/Bandage/wiki/Editing-graphs#merge-all-possible-nodes I'm currently...
I'd like to renumber the segments starting with `01` for the largest segment and proceeding to `99` for the smallest segment, zero-padding on the left with as many `0` as...
A GFA file ought to include both segments and gap records. It'd be preferable if gfakluge didn't segfault when encountering such a file. ``` H VN:Z:2.0 G * 6+ 50+...
This PR greatly simplifies the Makefile. I've removed some functionality, in particular building libgfakluge.a. Let me know if that functionality is needed, and I'll add it back.
Would you please tag a stable release that includes the `gfak fillseq` command? Thanks!
This question is more an xsltproc question than a taxon2newick question, but I'm hoping you might have a ready answer. The XML document returned by efetch is actually multiple concatenated...