RAILS v1.5.1

Remove samtools requirement (-p option) when running in "stream" (-s option) mode

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)

RAILS v1.4.2

Improved documentation, minor fixes, support for minimap2 (see runRAILSminimap.sh in the test folder)

cobbler/RAILS

remove hardcoded path to samtools from both scripts.
Added clarity to error message when empty array due to incompatible samtools version.

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

RAILS v1.3 and cobbler v0.4

Both scripts now take in file-of-filenames, instead of single files (query and alignment), as arguments

RAILS v1.2

bug fixes

RAILS v1.1 and cobbler v0.2, initial github release

RAILS and Cobbler: Scaffolding and automated finishing of draft genomes using long DNA sequences