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update for r350

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chhylp123
2021-07-26 00:16:00 -04:00
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.TH hifiasm 1 "16 April 2021" "hifiasm-0.15 (r327)" "Bioinformatics tools"
.TH hifiasm 1 "25 July 2021" "hifiasm-0.15.5 (r350)" "Bioinformatics tools"
.SH NAME
.PP
@@ -62,7 +62,7 @@ Hifiasm is an ultrafast haplotype-resolved de novo assembler for PacBio
Hifi reads. Unlike most existing assemblers, hifiasm starts from uncollapsed
genome. Thus, it is able to keep the haplotype information as much as possible.
The input of hifiasm is the PacBio Hifi reads in fasta/fastq format, and its
outputs consist of multiple types of assembly graph in GFA format.
outputs consist of multiple types of assembly graphs in GFA format.
.SH OPTIONS
@@ -104,17 +104,69 @@ Minimizer window size [51].
Number of bits for bloom filter; 0 to disable [37]. This bloom filter is used
to filter out singleton k-mers when counting all k-mers. It takes
.RI 2^( INT -3)
bytes of memory. A proper setting saves memory. 37 is recommended for human
assembly.
bytes of memory. A proper setting saves memory.
.BR -f37
is recommended for human
assembly. For small genomes, use
.BR -f0
to disable the initial bloom filter
which takes 16GB memory at the beginning. For genomes much larger
than human, applying
.BR -f38
or even
.BR -f39
is preferred to save memory on k-mer counting.
.TP
.BI -D \ INT
Drop k-mers occurring
.I >FLOAT*coverage
times [5.0].
Hifiasm discards these high-frequency k-mers
during error correction to reduce running time.
The
.I coverage
is determined automatically
by hifiasm based on k-mer plot, representing
homozygous read coverage. Raising this option
may improve the resolution of repetitive regions
but takes longer time.
.TP
.BI -N \ INT
Consider up to
.I max(-D*coverage,-N)
overlaps for each oriented read [100].
The
.I coverage
is determined automatically
by hifiasm based on k-mer plot, representing
homozygous read coverage. Raising this option may
improve the resolution of repetitive regions but
takes longer time.
.TP
.BI -r \ INT
Rounds of haplotype-aware error corrections [3]. This option affects all outputs of hifiasm.
Rounds of haplotype-aware error corrections [3].
This option affects all outputs of hifiasm.
Odd rounds of correction are preferred in practice.
.TP
.BI -z \ INT
Length of adapters that should be removed [0]. This option remove
.I INT
bases from both ends of each read.
Some old Hifi reads may consist of
short adapters (e.g., 20bp adapter at one end). For such data, trimming short adapters would
significantly improve the assembly quality.
.TP
.BI --min-hist-cnt \ INT
When analyzing the k-mer spectrum, ignore counts below
.IR INT .
.IR INT
[5]. For very low coverage of HiFi data, set smaller
value for this option.
.SS Assembly options
@@ -128,14 +180,6 @@ Note that unlike
.BR -r ,
this option does not affect error corrected reads and all-to-all overlaps.
.TP
.BI -z \ INT
Length of adapters that should be removed [0]. This option remove
.I INT
bases from both ends of each read.
Some old Hifi reads may consist of
short adapters (e.g., 20bp adapter at one end). For such data, trimming short adapters would
significantly improve the assembly quality.
.TP
.BI -m \ INT
@@ -149,10 +193,13 @@ section of this man-page.
.TP
.BI -p \ INT
Maximal probing distance for bubble popping when generating haplotype-resolved processed unitig graph
without small bubbles [100000]. Bubbles longer than
without small bubbles [0]. Bubbles longer than
.I INT
bases will not be popped. Small bubbles might be caused by somatic mutations or noise in data, which
are not the real haplotype information. For detailed description of this graph, please see the
bases will not be popped. Small bubbles might be caused by somatic mutations or noise in data.
Please note that hifiasm automatically pops small bubbles based on coverage,
which can be tweaked by
.BR --hom-cov .
For detailed description of this graph, please see the
.B OUTPUTS
section of this man-page.
@@ -163,13 +210,13 @@ A unitig is considered small if it is composed of less than
reads [3]. Hifiasm may try to remove small unitigs at various steps.
.TP
.BI -x \ FLOAT, -y \ FLOAT
.BI -x \ FLOAT1, -y \ FLOAT2
Max and min overlap drop ratio [0.8, 0.2]. This option is used with
.BR -r .
.BR -a .
Given a node
.I N
in the assembly graph, let max(N)
be the length of the largest overlap of
be the length of the longest overlap of
.I N.
Hifiasm iteratively drops overlaps of
.I N
@@ -179,17 +226,17 @@ are below a threshold controlled by
and
.BR -y .
Hifiasm applies
.B -r
.B -a
rounds of short overlap removal with an increasing threshold between
.B -x
.I FLOAT1
and
.BR -y .
.I FLOAT2.
.TP
.BI -i
Ignore error corrected reads and overlaps saved in
.IR prefix .*.bin
files.
files so that hifiasm will start again from scratch.
Apart from assembly graphs, hifiasm also outputs three binary files
that save all overlap information during assembly step.
With these files, hifiasm can avoid the time-consuming all-to-all overlap calculation step,
@@ -197,12 +244,24 @@ and do the assembly directly and quickly.
This might be helpful when users want to get an optimized assembly by multiple rounds of experiments
with different parameters.
.TP
.BI -u
Disable post-join step for contigs which may improve N50.
The post-join step of hifiasm improves contig N50 but may introduce misassemblies.
.TP
.BI --hom-cov \ INT
Homozygous read coverage inferred automatically in default. This option affects different types of outputs,
including Hi-C phased assembly and HiFi-only assembly.
.TP
.BI --pri-range \ INT1[,INT2]
Min and max coverage cutoff of primary contigs.
Keep contigs with coverage in this range at p_ctg.gfa.
Inferred automatically in default.
If INT2 is not specified, it is set to infinity.
If
.I INT2
is not specified, it is set to infinity.
Set -1 to disable.
.TP
@@ -286,41 +345,46 @@ but occurs <
.B -c
times in the other sample.
.TP
.BI --t-occ \ INT
Forcedly remove unitig including >
.I INT
unexpected haplotype-specific reads
without considering graph topology [60].
.SS Purge-dups options
.TP 10
.BI -l \ INT
Level of purge-dup. 0 to disable purge-dup, 1 to only purge contained haplotigs,
2 to purge all types of haplotigs, 3 to purge all types of haplotigs in most aggressive way
for high heterozygosity sample.
2 to purge all types of haplotigs, 3 to purge all types of haplotigs in most aggressive way.
In default, [3] for non-trio assembly, [0] for trio assembly.
For trio assembly, only level 0 and level 1 are allowed.
.TP
.BI -s \ FLOAT
Similarity threshold for duplicate haplotigs that should be purged [0.75 for -l1/-l2, 0.55 for -l3].
Similarity threshold for duplicate haplotigs that should be purged [0.75 for
.BR -l1/-l2 ,
0.55 for
.BR -l3 ].
.TP
.BI -O \ FLOAT
Min number of overlapped reads for duplicate haplotigs that should be purged [1].
.TP
.BI --purge-cov \ INT
.BI --purge-max \ INT
Coverage upper bound of Purge-dups, which is inferred automatically in default.
If the coverage of a contig is higher than this bound, don't apply Purge-dups.
If the coverage of a contig is higher than this bound, don't apply Purge-dups.
Larger value makes assembly more contiguous but may collapse repeats or segmental duplications.
.TP
.BI --n-hap \ INT
Assumption of haplotype number.
Assumption of haplotype number. If it is set to >2, the quality of
primary assembly for polyploid genomes might be improved.
.SS Debugging options
.TP 10
.B --dbg-gfa
Write additional files to speed up the debugging of graph cleaning.
.SS Hi-C-partition options [experimental, not stable]
@@ -347,6 +411,12 @@ phasing results but takes longer time.
Fraction to flip for perturbation [0.1]. Increasing this may improves
phasing results but takes longer time.
.TP
.BI --l-msjoin \ INT
Detect misjoined unitigs of >=
.I INT
in size; 0 to disable [500000].
.TP
.BI --seed \ INT
RNG seed [11].
@@ -367,23 +437,29 @@ haplotype-resolved raw unitig graph. This graph keeps all haplotype information.
.IR prefix .p_utg.gfa:
haplotype-resolved processed unitig graph without small bubbles. Small bubbles
might be caused by somatic mutations or noise in data, which are not the real
haplotype information. The size of popped small bubbles should be specified by
.BR -p .
haplotype information. Hifiasm automatically pops such small bubbles based on coverage.
The option
.BR --hom-cov
affects the result.
In addition, the option
.BR -p
forcedly pops bubbles.
.TP
*
.IR prefix .p_ctg.gfa:
assembly graph of primary contigs. This graph collapses different haplotypes.
assembly graph of primary contigs. This graph includes a complete assembly with
long stretches of phased blocks.
.TP
*
.IR prefix .a_ctg.gfa:
assembly graph of alternate contigs. This graph consists of all assemblies that
assembly graph of alternate contigs. This graph consists of all contigs that
are discarded in primary contig graph.
.TP
*
.IR prefix .hap*.p_ctg.gfa:
.IR prefix .*hap*.p_ctg.gfa:
phased contig graph. This graph keeps the phased assembly.
.RE
@@ -401,13 +477,13 @@ with trio-binning options:
.TP 2
*
.IR prefix .dip.hap1.p_ctg.gfa:
phased paternal/haplotype1 contig graph keeping the phased
fully phased paternal/haplotype1 contig graph keeping the phased
paternal/haplotype1 assembly.
.TP
*
.IR prefix .dip.hap2.p_ctg.gfa:
phased maternal/haplotype2 contig graph keeping the phased
fully phased maternal/haplotype2 contig graph keeping the phased
maternal/haplotype2 assembly.
.RE
@@ -418,17 +494,25 @@ With Hi-C partition options, hifiasm outputs:
.TP 2
*
.IR prefix .hic.p_ctg.gfa:
assembly graph of primary contigs. This graph collapses different haplotypes.
assembly graph of primary contigs.
.TP
*
.IR prefix .hic.hap1.p_ctg.gfa:
phased contig graph where each contig is fully phased.
fully phased contig graph where each contig is fully phased.
.TP
*
.IR prefix .hic.hap2.p_ctg.gfa:
phased contig graph where each contig is fully phased.
fully phased contig graph where each contig is fully phased.
.TP
*
.IR prefix .hic.a_ctg.gfa
(optional with
.BR --primary):
assembly graph of alternate contigs.
.RE
@@ -439,7 +523,7 @@ files:
and
.B *hic.tlb.bin.
Rerunning hifiasm with different Hi-C reads needs to delete these bin files
or enable
or use
.BR -i .
.RE
@@ -449,23 +533,23 @@ Hifiasm generates the following assembly graphs only with HiFi reads:
.RS 2
.TP 2
*
.IR prefix .p_ctg.gfa:
assembly graph of primary contigs. This graph collapses different haplotypes.
.IR prefix .bp.p_ctg.gfa:
assembly graph of primary contigs.
.TP
*
.IR prefix .bp.hap1.p_ctg.gfa:
balanced contig graph where each contig is partially phased.
partially phased contig graph of haplotype1.
.TP
*
.IR prefix .bp.hap2.p_ctg.gfa:
balanced contig graph where each contig is partially phased.
partially phased contig graph of haplotype2.
.RE
.PP
If the option
.BR -p
.BR -l0
or
.BR --primary
is specified, hifiasm outputs:
@@ -474,13 +558,12 @@ is specified, hifiasm outputs:
.TP 2
*
.IR prefix .p_ctg.gfa:
assembly graph of primary contigs. This graph collapses different haplotypes.
assembly graph of primary contigs.
.TP
*
.IR prefix .a_ctg.gfa:
assembly graph of alternate contigs. This graph consists of all assemblies that
are discarded in primary contig graph.
assembly graph of alternate contigs.
.RE