Add dataset demo

demo/assembly_graph.gfa

+H	VN:Z:1.0
+S	tig00000001	*	LN:i:2765793
+S	tig00000004	*	LN:i:1743974
+S	tig00000008	*	LN:i:256602

demo/readme.md

+# About dataset
+
+This is a 20x synthetic dataset created by LongISLND, with pacbio error model, on *Terriglobus roseus* (NC_108014.1).
+
+Assembled with canu 1.7.1 `genomeSize=5m --corOutCoverage=20`.
+
+# File description
+
+- assembly_contig.fasta: sequence of contig generate by canu
+- assembly_contig.gfa: contig graph generate by canu
+- reads_raw.fasta: read generated by LongISLND
+- reads_corrected.fasta: read corrected by canu
+
+# How to run knot
+
+On raw read:
+
+```
+knot -r demo/reads_raw.fasta -c demo/assembly_contig.fasta -g demo/assembly_graph.gfa -o raw
+```
+
+knot output are prefixed by `raw_`:
+```
+raw_AAG.csv                 # AAG format describe in Readme
+raw_knot                    # knot working directory
+├── contigs.fasta           # symbolic link to contig sequence provide as input
+├── contigs_filtred.fasta   # contig keept in analysis filter on length
+├── contigs_filtred.gfa     # contig graph generate by fpa on contig mapping (contigs_filtred.paf)
+├── contigs_filtred.paf     # mapping of filtred contig with minimap
+├── contigs_graph.gfa       # symbolic link to contig graph provide as input
+├── ext_search.csv          # read associated to each contig extremity
+├── raw_reads.fasta         # symbolic link to raw read provide as input
+├── raw_reads.paf           # self mapping of raw_reads
+├── raw_reads_splited.fasta # raw reads without not covered sequence provide by yacrd
+├── raw_reads_splited.gfa   # overlap graph generate by fpa on raw_reads_splited self mapping
+├── raw_reads_splited.paf   # self mapping of raw_reads_splited
+├── raw_reads.yacrd         # yacrd output on raw_reads
+└── read2asm.paf            # mapping of read on contigs_filtred
+```
+
+On corrected read:
+
+```
+knot -C demo/reads_raw.fasta -c demo/assembly_contig.fasta -g demo/assembly_graph.gfa -o raw
+```
+
+knot output are prefixed by `corrected_`:
+```
+corrected_AAG.csv           # AAG format describe in Readme
+corrected_knot              # knot working directory
+├── contigs.fasta           # symbolic link to contig sequence provide as input
+├── contigs_filtred.fasta   # contig keept in analysis, filter on length
+├── contigs_filtred.gfa     # contig graph generate by fpa on contig mapping (contigs_filtred.paf)
+├── contigs_filtred.paf     # mapping of filtred contig with minimap
+├── contigs_graph.gfa       # symbolic link to raw read provide as input
+├── ext_search.csv          # read associated to each contig extremity
+├── raw_reads_splited.fasta # symbolic link to corrected read provide as input
+├── raw_reads_splited.gfa   # overlap graph generate by fpa on raw_reads_splited self mapping
+├── raw_reads_splited.paf   # self mappig of raw_reads_splited
+└── read2asm.paf            # mapping of read on contigs_filterd
+```