Tools for haplotype-wise reconstruction of pseudomolecules
Version V1 is on its way with a more features and a more refined workflow
The aim of the tool is improving continuity of a given genome draft assembly up to pseudomolecule representation using a closely relate species as guide to sort and direct the query sequences.
Despite the recent advance in sequencing technologies allowing less fragmented assemblies, achieving a chromosome scale representation is still challenging. By using a closely related species as a guide, the tool aims at use the conserved genomic structures to sort and direct the given sequences, then a representation of the pseudomolecules is given as a non-redundant tiling path of the query assembly
When dealing with heterozygous genomes, picturing the full genomic variability in a diploid representation adds a second layer of complexity. A way to deal with the issue is to haploidize the assembly, but, while complexity is actually reduced, this leads to loss of information on the "alternative" state.
Moreover, some tools do not deliver phasing information, it is lost during the assembly pipeline or innacurate because of haplotype switches. Even more difficult is the situation of high heterozygosity rates that do trick the assembly tools in overestimating the the "primary" assembly or, better, underestimating the genomic variability, ending in imperfect primary/alternative sequence paring information.
The tool takes care of segregating sequences that do actually represent alternatives to the very same genomic locus. A reconstruction of pseudomolecules is then performed caring of separate usage of the alternative sequences in different tiling paths
- Python libraries
- Python ver >2.7
- networkx ver >2.1 (previous version are incompatible due to missing functions)
- Biopython
- External tools
file.paf: Query to reference alignment file. Reusable- Tiling path #1:
out.1.agp: AGP file describing output sequences in function of input query used to assemble themout.1.fasta: Output sequences in FASTA formatout.1.list: Sorted and directed list of input query used
- Tiling path #2 (if
--N2is not set)out.2.agp: AGP file describing output sequences in function of input query used to assemble themout.2.fasta: Output sequences in FASTA formatout.2.list: Sorted and directed list of input query used
- Unplaced sequences
out.Un.agp: AGP file describing unplaced sequences in function of unused input query in any tiling pathout.Un.fasta: Unplaced sequences in FASTA formatout.Un.list: List of unused input query sequences
List files, like the ones delivered as output, can be used to control the reconstruction procedure through -1, -2, --B1, --B2, --R1, and --R2 parameters
- Intermediate mapping files:
- tmp.map1.paf.for
- tmp.map1.paf.multimapping
- tmp.map1.paf.multimapping.uniq
- tmp.map1.paf.rev
HaploSplit.py [-h] [-i file.paf [Required]]
[-r reference.fasta [Required]]
[-q query.fasta [Required]] [-v] [-o NAME] [-p PREFIX]
[-a] [-f] [-g N] [-c N] [--distance1 N] [--distance2 N]
[-m] [-u] [-t "minimap2 --cs -t 4 -x asm20 -r 1000"]
[-n N] [-1 1st.txt] [-2 2nd.txt] [--R1 1st.txt]
[--min1 N] [--R2 2nd.txt] [--min2 N] [--B1 2nd.txt]
[--B2 2nd.txt] [--N2]
-h, --help show this help message and exit
-i file.paf [Required], --input file.paf [Required]
File of hits. Used as input if already mapped, output
result of mapping procedure if -m/--map
-r reference.fasta [Required], --reference reference.fasta [Required]
FASTA file with reference sequence
-q query.fasta [Required], --query query.fasta [Required]
FASTA file with query sequence
-v, --dry Dry run: find best tiling paths and excluded nodes but
no FASTA or AGP exported
-o NAME, --out NAME Output NAME prefix for files [default: out]
-p PREFIX, --prefix PREFIX
Output NAME prefix for files [default: NEW]
-a, --agp Export paths in AGP format to NAME.{1,2,Un}.agp
-f, --fasta Export paths sequences in NAME.{1,2,Un}.fasta
-g N, --gapsize N Minimum gap size placeholder for AGP and FASTA (in bp)
[default: 1,000bp]
-c N, --concatenate N
Set the gap size used to concatenate unplaced
sequences (in bp) [default: do not concatenated]
--distance1 N Set the maximum distance (bp) between two hits to be
considered adjacent [default: 2,000,000bp]
--distance2 N Set the maximum distance (bp) between two hits to be
considered adjacent at second round [default:
4,000,000bp]
-m, --map Do run mapping [overwrite input file.paf if existing]
-u, --uniq Map only
-t "minimap2 --cs -t 4 -x asm20 -r 1000", --tool "minimap2 --cs -t 4 -x asm20 -r 1000"
Mapping command for minimap2
-n N, --hitgap N Allowed gap between hits to be merged [default:
500000]
-1 1st.txt, --path1 1st.txt
Use ONLY the following list of (stranded) contigs to
create the first haplotype. Tab separated file with
Target_ID followed by comma separated list of contigs
(contig1,contig2,[...],contigN)
-2 2nd.txt, --path2 2nd.txt
Use ONLY the following list of (stranded) contigs to
create the second haplotype. Tab separated file with
Target_ID followed by comma separated list of contigs
(contig1,contig2,[...],contigN)
--R1 1st.txt Require to use the following list of (stranded)
contigs in the first haplotype. Tab separated file
with Target_ID followed by comma separated list of
contigs (contig1,contig2,[...],contigN)
--min1 N Minimum length of sequence allowed to be a requirement
for the first haplotype (default: 0)
--R2 2nd.txt Require to use the following list of (stranded)
contigs in the second haplotype. Tab separated file
with Target_ID followed by comma separated list of
contigs (contig1,contig2,[...],contigN)
--min2 N Minimum length of sequence allowed to be a requirement
for the second haplotype (default: 0)
--B1 2nd.txt Blacklisted (stranded) contigs NOT to be used in the
first haplotype. Tab separated file with Target_ID
followed by comma separated list of contigs
(contig1,contig2,[...],contigN)
--B2 2nd.txt Blacklisted (stranded) contigs NOT to be used in the
second haplotype. Tab separated file with Target_ID
followed by comma separated list of contigs
(contig1,contig2,[...],contigN)
--N2 Don't run the search for the 2nd path