Update readme

Readme.md

@@ -2,11 +2,11 @@
 
 KNOT: Knowledge Network Overlap exTraction is a tool for the investigation of fragmented long read assemblies.
 
-Give an assembly and a set of reads to KNOT, it will output an information-rich contig graph in GFA format that tells you about adjacencies between contigs.
+Give an assembly and a set of reads to KNOT, it will output an information-rich contig graph in CSVformat that tells you about adjacencies between contigs.
 
 ## Input
 
-1) long reads (corrected or not) FASTQ
+1) long reads (corrected or not) FASTA (no FASTQ allowed)
 2) assembly graph (in gfa1) produced by an assembler
 3) and contigs (in fasta) from the same assembler
 
@@ -15,10 +15,15 @@ Give an assembly and a set of reads to KNOT, it will output an information-rich
 KNOT outputs an Augmented Assembly Graph (AAG). The AAG is a directed graph where nodes are contigs. An edge is present if two contigs overlap or, if in the original string graph of the reads, 
 there exists a path between extremities of both contigs.
 
-Output format (csv):
-```
-tig1 extremity, read of extremity of tig1, tig2 extremity, read of extremity of tig2, length of path between both extremities, number of reads in path mapped against contigs 
-```
+Output format is in CSV format with 8 column:
+1. tig1: tig name and extremity use in format {tig name}\_{extremity} e.g. tig00000001\_begin
+2. read1: read id use to search path for tig1 extremity
+3. tig2: other tig name and extremity
+4. read2: read id use to search path for tig2 extremity
+5. nb_read: nb\_read in path between read1 and read2 (include)
+6. nb_base: nb\_base in path between read2 and read2
+7. paths: id of read in path found between read1 and read2, separated by ;
+8. nbread_contig: number of read assign for each contig in format {tig name}:{nb of read in paths assign to contig}/{nb of read in tig} not\_assign used to read not assigned to a contig, separated by ;.
 
 This output can be used to manually investigate the result of an assembly.
 Short paths between contigs are likely true adjacencies. Long paths are likely repeat-induced.
@@ -42,10 +47,34 @@ You can use corrected long reads in place of raw_reads with `-m` option.
 
 Full command line usage:
 ```
-
-```
-
-In addition, snakemake parameters can be used.
+usage: KNOT [-h] -c CONTIGS [-g CONTIGS_GRAPH]
+            (-r RAW_READS | -C CORRECT_READS) -o OUTPUT
+            [--search-mode {base,node}]
+            [--contig-min-length CONTIG_MIN_LENGTH] [--read-type {pb,ont}]
+            [--help-all]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTIGS, --contigs CONTIGS
+                        fasta file than contains contigs
+  -g CONTIGS_GRAPH, --contigs_graph CONTIGS_GRAPH
+                        contigs graph
+  -r RAW_READS, --raw-reads RAW_READS
+                        read used for assembly
+  -C CORRECT_READS, --correct-reads CORRECT_READS
+                        read used for assembly
+  -o OUTPUT, --output OUTPUT
+                        output prefix
+  --search-mode {base,node}
+                        what path search optimize, number of base or number of
+                        node
+  --contig-min-length CONTIG_MIN_LENGTH
+                        contig with size lower this parameter are ignored
+  --read-type {pb,ont}  type of input read, default pb
+  --help-all            show knot help and snakemake help
+```
+
+In addition, snakemake parameters can be add after `--`.
 
 ## Installation
 
@@ -83,8 +112,6 @@ Instruction:
 pip3 install git+https://gitlab.inria.fr/pmarijon/knot.git 
 ```
 
-
-
 ## How to update an already-installed KNOT?
 
 ### Conda installation
@@ -104,7 +131,6 @@ conda env create -f conda_env.yml
 pip3 install --upgrade git+https://gitlab.inria.fr/pmarijon/knot.git
 ```
 
-
 # Description of the pipeline
 
 ![Globale pipeline](images/pipeline.png)
@@ -117,8 +143,43 @@ Legend:
 - output `#5D2971`
 - pipeline internal tool `#FFD300`
 
-
+# All output description
+
+If you run knot with raw reads:
+```
+{output prefix}_AAG.csv     # AAG result in format describe earlier
+{output prefix}_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
+```
+
+If you run knot with corrected reads:
+```
+{output prefix}_AAG.csv     # AAG result in format describe earlier
+{output prefix}_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
+```
 
 # Citation
 
-Please cite this Github URL for now, manuscript is in submission.
\ No newline at end of file
+Please cite this Github URL for now, manuscript is in submission.

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
+```
+
+On corrected read:
+
+```
+knot -C demo/reads_raw.fasta -c demo/assembly_contig.fasta -g demo/assembly_graph.gfa -o raw
+```

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
-```