Rayan Chikhi
Rayan Chikhi
Hi Ryan, We'll release a software around next month where we'll need a feature that is present in the development branch of Bandage. By any chance, do you plan on...
Hi Ryan, Do you have plans to implement a graphical way to visualize e.g. a contig as a line that goes along multiple nodes? e.g. using CSV information.
When BLASTing a bacterial reference against a large set of contigs, Bandage will report by default only 250 hits per chromosome, which might be a small subset of the contigs....
Hi! Thanks for this very nice piece of software. Bandage really needs a "undo" action. Whenever I delete a node by mistake, or move a node by mistake, etc..
Hi, I very much look forward to use dashing, however three small issues with how it is distributed made me lose some time during installation: 1) source code is huge...
This describes the gathering of all the assemblies generated by Serratus into a single file. TLDR: It's available at https://lovelywater2.s3.amazonaws.com/assembly/rdva/rdva_v0.2.fa.lz4 (updated 2022-05-14) * Number of accessions assembled: 58,557 * 3.1...
List of the **1,000** random SRAs accessions: `s3://serratus-rayan/1krandom-assembly/1000_random_sra.txt` (obtained through: `cat novel_id90.fa | grep ">" | cut -c 2- |sort |uniq | shuf -n 1000`) **952** SPAdes log files were...
This issues describes the procedure to search all of our contigs against RdRP and presents results. (Slack thread: https://hackseq-rna.slack.com/archives/C012H9SDQCA/p1615948152031200) Input: FASTA files of contigs, either assembled using micro (all SRA...
List of the 990 accessions where there's possibly a new CoV/nido RdRp according to `sra_species_table.tsv`: `s3://serratus-rayan/pro_new_cov_nido-assembly/all_new_cov_nido.sra` **900** could be assembled, here are the: * `scaffolds.fasta` (900) : `s3://serratus-rayan/pro_new_cov_nido-assembly/all_new_cov_nido.scaffolds.txt` * `gene_clusters.fasta`...
This thread will be for updates of the `.pro` assemblies. number of `.pro.gz` files analyzed (all of s3://serratus-public/out/21* except \*r1p\*): **5,726,283** number of `.fasta.gz` obtained after converting `.pro` to FASTA...