xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-10-10 00:30:55 +08:00
Code Issues Packages Projects Releases Wiki Activity

update readme

Browse Source
This commit is contained in:
chhylp123
2020-06-27 10:57:22 -04:00
parent 71f6c93d58
commit 449950cddb
2 changed files with 6 additions and 11 deletions
Download Patch File Download Diff File Expand all files Collapse all files
Overlaps.cpp
+1 -5
View File
@@ -26123,7 +26123,6 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
memset(R_INF.trio_flag, AMBIGU, R_INF.total_reads*sizeof(uint8_t)); memset(R_INF.trio_flag, AMBIGU, R_INF.total_reads*sizeof(uint8_t));
} }
///print_binned_reads(sources, n_read, coverage_cut); ///print_binned_reads(sources, n_read, coverage_cut);
clean_weak_ma_hit_t(sources, reverse_sources, n_read); clean_weak_ma_hit_t(sources, reverse_sources, n_read);
@@ -26136,8 +26135,6 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
ma_hit_flt(sources, n_read, coverage_cut, max_hang_length, mini_overlap_length); ma_hit_flt(sources, n_read, coverage_cut, max_hang_length, mini_overlap_length);
///fix_binned_reads(sources, n_read, coverage_cut); ///fix_binned_reads(sources, n_read, coverage_cut);
///just need to deal with trio here ///just need to deal with trio here
ma_hit_contained_advance(sources, n_read, coverage_cut, ruIndex, max_hang_length, mini_overlap_length); ma_hit_contained_advance(sources, n_read, coverage_cut, ruIndex, max_hang_length, mini_overlap_length);
@@ -26145,7 +26142,6 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
asg_arc_del_trans(sg, gap_fuzz); asg_arc_del_trans(sg, gap_fuzz);
asm_opt.coverage = get_coverage(sources, coverage_cut, n_read); asm_opt.coverage = get_coverage(sources, coverage_cut, n_read);
if(VERBOSE >= 1) if(VERBOSE >= 1)
{ {
char* unlean_name = (char*)malloc(strlen(output_file_name)+25); char* unlean_name = (char*)malloc(strlen(output_file_name)+25);
@@ -26156,7 +26152,6 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
asg_cut_tip(sg, asm_opt.max_short_tip); asg_cut_tip(sg, asm_opt.max_short_tip);
///drop_inexact_edegs_at_bubbles(sg, bubble_dist); ///drop_inexact_edegs_at_bubbles(sg, bubble_dist);
if(clean_round > 0) if(clean_round > 0)
@@ -26174,6 +26169,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
int i = 0; int i = 0;
for (i = 0; i < clean_round; i++, drop_ratio += cut_step) for (i = 0; i < clean_round; i++, drop_ratio += cut_step)
{ {
if(drop_ratio > max_ovlp_drop_ratio) if(drop_ratio > max_ovlp_drop_ratio)
{ {
drop_ratio = max_ovlp_drop_ratio; drop_ratio = max_ovlp_drop_ratio;
README.md
+3 -4
View File
@@ -46,15 +46,14 @@ assembly by multiple rounds of experiments with different parameters.
Hifiasm is a standalone and lightweight assembler, which does not need external Hifiasm is a standalone and lightweight assembler, which does not need external
libraries (except zlib). For large genomes, it can generate high-quality libraries (except zlib). For large genomes, it can generate high-quality
assembly in a few hours. Hifiasm has been tested on human, butterfly, rice and drosophila. assembly in a few hours. Hifiasm has been tested on various large and complex datasets.
In particular, hifiasm is able to assemble the 26.5Gb California redwood tree in a few days.
The results are as follows: The results are as follows:
|<sub>Dataset<sub>|<sub>GSize<sub>|<sub>Cov<sub>|<sub>Asm options<sub>|<sub>CPU time<sub>|<sub>Wall time<sub>|<sub>RAM<sub>|<sub>[unitig][unitig]/[contig][unitig] N50<sup>[1]</sup><sub>| |<sub>Dataset<sub>|<sub>GSize<sub>|<sub>Cov<sub>|<sub>Asm options<sub>|<sub>CPU time<sub>|<sub>Wall time<sub>|<sub>RAM<sub>|<sub> N50<sub>|
|:---------------|-----:|-----:|:---------------------|-------:|--------:|----:|----------------:| |:---------------|-----:|-----:|:---------------------|-------:|--------:|----:|----------------:|
|<sub>[\[Mouse (C57/BL6J)\]](https://www.ncbi.nlm.nih.gov/sra/?term=SRR11606870)<sub>|<sub>2.7Gb<sub>|<sub>x25<sub>|<sub>-t48 -l0<sub>|<sub>172.9h<sub>|<sub>4.8h<sub>|<sub>76G<sub>|<sub>20.6Mb<sub>|
|<sub>[\[Redwood\]](https://downloads.pacbcloud.com/public/dataset/redwood2020/)<sub>|<sub>26.5Gb<sub>|<sub>x23<sub>|<sub>-k 40 -t 64 -r 2<sub>|<sub>7274h30m<sub>|<sub>141h30m<sub>|<sub>512G<sub>|<sub>1.7Mb/1.9Mb<sub>| |<sub>[\[Redwood\]](https://downloads.pacbcloud.com/public/dataset/redwood2020/)<sub>|<sub>26.5Gb<sub>|<sub>x23<sub>|<sub>-k 40 -t 64 -r 2<sub>|<sub>7274h30m<sub>|<sub>141h30m<sub>|<sub>512G<sub>|<sub>1.7Mb/1.9Mb<sub>|
<sub>[1] unitig N50 is the N50 of assembly graph with haplotype information (i.e., bubbles), while the contig N50 is the N50 of haplotype collapsed assembly (i.e., without bubbles).<sub>
## Usage ## Usage