Recent Releases of RAILS and Cobbler
RAILS and Cobbler - RAILS v1.5.1
Remove samtools requirement (-p option) when running in "stream" (-s option) mode
Scientific Software - Peer-reviewed
- Perl
Published by warrenlr almost 7 years ago
RAILS and Cobbler - RAILS v1.5.0
Ability to stream the .sam output of your favorite aligner directly into cobbler/RAILS (tested with minimap2/human data -- see runRAILSminimapSTREAM.sh)
Scientific Software - Peer-reviewed
- Perl
Published by warrenlr almost 7 years ago
RAILS and Cobbler - RAILS v1.4.2
Improved documentation, minor fixes, support for minimap2 (see runRAILSminimap.sh in the test folder)
Scientific Software - Peer-reviewed
- Perl
Published by warrenlr about 7 years ago
RAILS and Cobbler - cobbler/RAILS
remove hardcoded path to samtools from both scripts. Added clarity to error message when empty array due to incompatible samtools version.
Scientific Software - Peer-reviewed
- Perl
Published by warrenlr about 8 years ago
RAILS and Cobbler - RAILS v1.4 and cobbler v0.5
RAILS v1.4 and cobbler v0.5 Overall better read handling for gap-filling and scaffolding 1. Save in memory gap sequence (patch), from highest-matching read for both tools 2. Track #reads support in cobbler (-l) and RAILS, and allow cutoff when scaffolding (-l and -a), with latter (RAILS) 3. Remove the hardcoded two-hit requirement for a read in RAILS. Instead, process two best hits for each read aligning different sequences 4. Implement grace (-g) option, which effectively simulate read trimming (valuable for ONT mapping) 5. bug fixes (-list.tsv (cobbler) reported some instances of gap-fill regions not fixed in the assembly – very marginal ~2.4% discrepancy). cobbler gap-fill table now lists the number of supporting reads for each gap filled
Scientific Software - Peer-reviewed
- Perl
Published by warrenlr over 8 years ago
RAILS and Cobbler - RAILS v1.3 and cobbler v0.4
Both scripts now take in file-of-filenames, instead of single files (query and alignment), as arguments
Scientific Software - Peer-reviewed
- Perl
Published by warrenlr over 8 years ago
RAILS and Cobbler - RAILS v1.2
bug fixes
Scientific Software - Peer-reviewed
- Perl
Published by warrenlr over 8 years ago
RAILS and Cobbler - RAILS v1.1 and cobbler v0.2, initial github release
RAILS and Cobbler: Scaffolding and automated finishing of draft genomes using long DNA sequences
Scientific Software - Peer-reviewed
- Perl
Published by warrenlr over 9 years ago