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update readme

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chhylp123
2020-06-27 10:57:22 -04:00
parent 71f6c93d58
commit 449950cddb
2 changed files with 6 additions and 11 deletions
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Overlaps.cpp
+3 -7
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@@ -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));
}
///print_binned_reads(sources, n_read, coverage_cut);
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);
///fix_binned_reads(sources, n_read, coverage_cut);
///just need to deal with trio here
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);
asm_opt.coverage = get_coverage(sources, coverage_cut, n_read);
if(VERBOSE >= 1)
{
char* unlean_name = (char*)malloc(strlen(output_file_name)+25);
@@ -26155,10 +26151,9 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
}
asg_cut_tip(sg, asm_opt.max_short_tip);
///drop_inexact_edegs_at_bubbles(sg, bubble_dist);
if(clean_round > 0)
{
double cut_step;
@@ -26174,6 +26169,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
int i = 0;
for (i = 0; i < clean_round; i++, drop_ratio += cut_step)
{
if(drop_ratio > max_ovlp_drop_ratio)
{
drop_ratio = max_ovlp_drop_ratio;
@@ -26282,7 +26278,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
debug_ma_hit_t(reverse_sources, coverage_cut, n_read, max_hang_length,
mini_overlap_length);
**/
///note: don't apply asg_arc_del_too_short_overlaps() after this function!!!!
rescue_contained_reads_aggressive(NULL, sg, sources, coverage_cut, ruIndex, max_hang_length,
mini_overlap_length, bubble_dist, 10, 1, 0, NULL, NULL);
README.md
+3 -4
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@@ -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
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.
In particular, hifiasm is able to assemble the 26.5Gb California redwood tree in a few days.
assembly in a few hours. Hifiasm has been tested on various large and complex datasets.
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>[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