tar -zxvf Gap-Aidv1.1.tar.gz
cd Gap-Aidv1.1
chmod +x Gap-Aidv1.1
./Gap-Aidv1.1The preprocess program can only be used on Linux systems
cd Gap-Aid/preprocess/pipeline.sh
chmod + x pipeline.shRun pipeline.sh with full paths or add pipeline.sh to environment PATH
version 240720
USAGE: ./pipeline.sh [options] <path_to_input_chromosomes> <path_to_input_reads>
DESCRIPTION:
This is a script that maps reads to draft assemblies and get the overlaps of reads
ARGUMENTS:
path_to_input_chromosomes Specify path to draft assembly fasta file.
path_to_input_reads Specify file path to raw reads file.
OPTIONS:
-p|--prefix The prefix of output. (default:gap-aid)
-r|--reads_type The reads type. (default:hifi)
-m|--mask The length of the proximity gap you want to mask (default:500000).
-c|--contig Specify path to assembly fasta file.
-re|--reliable The alignment you think are reliable ,format:'MapQ aligned_ratio'.(default:'10 0.6')
-l|--length The Alignment block length you think are unreliable.(default:500)
-f|--filter Do you want to filter the alignment? yes/no (default:no)
-z|--zip Do you want to compressed the alignment file with gzip ? yes/no (default:no)
-t|--threads Number of threads(default:4)
--aligner minimap2/winnowmap(default:minimap2)
--map_arg map args ex:'-x map-hifi';
arg must be wraped by ' '
--minimap2 Installed minimap2 path
--winnowmap Installed winnowmap path
--seqkit Installed seqkit path
--jellyfish Installed jellyfish path
--rafilter Installed rafilter path
-h|--help Shows this help. Type --help for a full set of options.
*****************************************************the raw reads file must be fatsa format,any compressed files are not supported
| Short Parameter | Long Parameter | Description |
|---|---|---|
| -p | --prefix | The prefix of output files. |
| -r | --reads_type | The reads type. You can choose hifi or ont. (default:hifi) |
| -m | --mask | To avoid the influence of repeated sequences near the gap, you can choose to mask the sequences before and after the gap. The default length is 500k |
| -c | --contig | Contigs used to assemble scaffolds to obtain more comprehensive kmer information |
| -re | --reliable | Use alignment length and alignment quality to filter alignments. By default, alignments with mapq>10 and alignment ratio(alignment ratio=Alignment block length / reads sequence length) greater than 0.6 are considered high-quality alignments. In non-gap regions, the reads corresponding to such alignments will be filtered out. |
| -l | --length | The Alignment block length you think are unreliable.(default:500)By default, alignments with alignment block length less than 500bp will be discarded. |
| -f | --filter | Do you want to filter the conflict alignments? (yes or no default:no ) This will use a dynamic programming algorithm to remove some of the conflicting alignments, which has a high memory requirement |
| -z | --zip | Do you want to compressed the alignment file with gzip ? This will make the file smaller but will take more time.(yes or no default:no ) |
The files needed by Gap-aid are in the $prefix_workdir
There are 12 files.
*.chr.fa is the scaffold that your input
reads.\ is filtered reads
*infor.txt is the scaffold gap information
map.final.paf\ is the alignments of scaffold and reads
ovlp.final.paf\ is the alignments of reads and reads
.score.txt\ is the score we use to recommend the reads
example.tar.gz is an example for Gap-Aid, it applies to visualization programs, not to preprocessing programs.
usage:
tar -zxvf example.tar.gz
#Select the example directory in the Gap-AidGap-Aidv1.1 is a binary program under Linux.(Required a GUI or a remote GUI such as X11.)
Run Gap-Aidv1.1 Under the Gap-Aidv1.1 folder
Gap-Aidv1.1 compiled by gcc9.4.0,too low gcc version may cause problems.
Gap-Aidv1.1.exe is a binary program under windows.