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bug fixed

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chhylp123
2021-04-17 00:31:19 -04:00
parent efacf8e796
commit 4bc43cec92
3 changed files with 88 additions and 42 deletions
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hifiasm.1
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@@ -1,4 +1,4 @@
.TH hifiasm 1 "20 Mar 2021" "hifiasm-0.14.2 (r315)" "Bioinformatics tools"
.TH hifiasm 1 "16 April 2021" "hifiasm-0.15 (r327)" "Bioinformatics tools"
.SH NAME
.PP
@@ -349,11 +349,7 @@ RNG seed [11].
.SH OUTPUTS
.PP
Without trio partition options
.B -1
and
.BR -2 ,
hifiasm generates the following assembly graphs in the GFA format:
In general, hifiasm generates the following assembly graphs in the GFA format:
.RS 2
.TP 2
@@ -380,40 +376,106 @@ assembly graph of primary contigs. This graph collapses different haplotypes.
assembly graph of alternate contigs. This graph consists of all assemblies that
are discarded in primary contig graph.
.TP
*
.IR prefix .hap*.p_ctg.gfa:
phased contig graph. This graph keeps the phased assembly.
.RE
.PP
With trio partition, hifiasm outputs the following assembly graphs:
Hifiasm outputs
.B *.r_utg.gfa
and
.B *.p_utg.gfa
in any cases.
Specifically, hifiasm outputs the following assembly graphs
with trio-binning options:
.RS 2
.TP 2
*
.IR prefix .dip.r_utg.gfa:
haplotype-resolved raw unitig graph. This graph keeps all haplotype information.
.TP
*
.IR prefix .hap1.p_ctg.gfa:
phased paternal/haplotype1 contig graph. This graph keeps the phased
.IR prefix .dip.hap1.p_ctg.gfa:
phased paternal/haplotype1 contig graph keeping the phased
paternal/haplotype1 assembly.
.TP
*
.IR prefix .hap2.p_ctg.gfa:
phased maternal/haplotype2 contig graph. This graph keeps the phased
.IR prefix .dip.hap2.p_ctg.gfa:
phased maternal/haplotype2 contig graph keeping the phased
maternal/haplotype2 assembly.
.RE
.PP
With Hi-C partition, hifiasm outputs the assembly graphs like trio partition,
but with additional prefix
.B [hic].
In this mode, hifiasm keeps Hi-C alignment results and Hi-C index in two bin
With Hi-C partition options, hifiasm outputs:
.RS 2
.TP 2
*
.IR prefix .hic.p_ctg.gfa:
assembly graph of primary contigs. This graph collapses different haplotypes.
.TP
*
.IR prefix .hic.hap1.p_ctg.gfa:
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.
.RE
.PP
Hifiasm keeps Hi-C alignment results and Hi-C index in two bin
files:
.B *hic.lk.bin
and
.B *hic.tlb.bin.
Rerunning hifiasm with different Hi-C reads needs to delete these bin files.
Rerunning hifiasm with different Hi-C reads needs to delete these bin files
or enable
.BR -i .
.RE
.PP
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.
.TP
*
.IR prefix .bp.hap1.p_ctg.gfa:
balanced contig graph where each contig is partially phased.
.TP
*
.IR prefix .bp.hap2.p_ctg.gfa:
balanced contig graph where each contig is partially phased.
.RE
.PP
If the option
.BR -p
or
.BR --primary
is specified, hifiasm outputs:
.RS 2
.TP 2
*
.IR prefix .p_ctg.gfa:
assembly graph of primary contigs. This graph collapses different haplotypes.
.TP
*
.IR prefix .a_ctg.gfa:
assembly graph of alternate contigs. This graph consists of all assemblies that
are discarded in primary contig graph.
.RE