For this example we will use the directory 01_clean_reads previously created with the clean module. We run the following Captus command to assemble our cleaned reads:
We are including the option --sample_reads_target 1000000 to show the expected output even though this option will not be very commonly used. Additionally, the option --max_contig_gc 60.0 is used to filter contigs with GC content over 60% after assembly, only when this option is used the file filtered_contigs.fasta is produced.
After the run is finished we should see a new directory called 02_assemblies with the following structure and files:
1. [sample]__captus-asm
A subdirectory ending in __captus-asm is created to contain the assembly of each sample separately (S1, S2, S3, and S4 in the image).
2. 00_subsampled_reads
This directory is only created when the option --sample_reads_target is used. It contains the subsampled reads in FASTQ format that were used for the assembly.
3. 01_assembly
This directory contains the FASTA and FASTG assembly files as well as assembly statistics and logs.
4. assembly.fasta
The main assembly file in FASTA format, this file contains the contigs assembled by MEGAHIT. The sequence headers are modified by Captus to resemble the headers produced by the assembler Spades.
5. assembly_graph.fastg
The assembly graph in FASTG format. This file can be explored in Bandage or similar software which are able to plot the connections between contigs, loops, circular segments, etc.
6. filtered_contigs.fasta
This file in only created when the option --max_contig_gc is used, Captus will place any contig exceeding the specified GC content in this FASTA-formatted file (same format as in 4).
7. assembly.stats.tsv, assembly.stats.t.tsv
Assembly statistics, the assembly.stats.t.tsv is just a transposed version of assembly.stats.tsv:
MEGAHIT program logs, the brief version contains just the screen output from each MEGAHIT run.
megahit.brief.log
Captus' MEGAHIT Command:
megahit -1 /Volumes/Shuttle500G/for_docs_output/02_assemblies/GenusA_speciesA_CAP__captus-asm/00_subsampled_reads/GenusA_speciesA_CAP_R1.fq.gz -2 /Volumes/Shuttle500G/for_docs_output/02_assemblies/GenusA_speciesA_CAP__captus-asm/00_subsampled_reads/GenusA_speciesA_CAP_R2.fq.gz --min-count 2 --k-list 31,39,47,63,79,95,111,127,143,159,175 --merge-level 20,0.95 --prune-level 2 --memory 8504035246 --num-cpu-threads 4 --out-dir /Volumes/Shuttle500G/for_docs_output/02_assemblies/GenusA_speciesA_CAP__captus-asm/01_assembly --min-contig-len 182 --tmp-dir /Users/emortiz/captus_megahit_tmp
2022-04-08 01:09:30 - MEGAHIT v1.2.9
2022-04-08 01:09:30 - Using megahit_core with POPCNT and BMI2 support
2022-04-08 01:09:30 - Convert reads to binary library
2022-04-08 01:09:31 - b'INFO sequence/io/sequence_lib.cpp : 77 - Lib 0 (/Volumes/Shuttle500G/for_docs_output/02_assemblies/GenusA_speciesA_CAP__captus-asm/00_subsampled_reads/GenusA_speciesA_CAP_R1.fq.gz,/Volumes/Shuttle500G/for_docs_output/02_assemblies/GenusA_speciesA_CAP__captus-asm/00_subsampled_reads/GenusA_speciesA_CAP_R2.fq.gz): pe, 720090 reads, 151 max length'
2022-04-08 01:09:31 - b'INFO utils/utils.h : 152 - Real: 1.3603\tuser: 0.6603\tsys: 0.2130\tmaxrss: 64000000'
2022-04-08 01:09:31 - Start assembly. Number of CPU threads 4
2022-04-08 01:09:31 - k list: 31,39,47,63,79,95,111,127,143,159,175
2022-04-08 01:09:31 - Memory used: 8504035246
2022-04-08 01:09:31 - Extract solid (k+1)-mers for k = 31
2022-04-08 01:09:41 - Build graph for k = 31
2022-04-08 01:09:43 - Assemble contigs from SdBG for k = 31
2022-04-08 01:09:46 - Local assembly for k = 31
2022-04-08 01:09:55 - Extract iterative edges from k = 31 to 39
2022-04-08 01:09:57 - Build graph for k = 39
2022-04-08 01:09:58 - Assemble contigs from SdBG for k = 39
2022-04-08 01:10:00 - Local assembly for k = 39
2022-04-08 01:10:15 - Extract iterative edges from k = 39 to 47
2022-04-08 01:10:17 - Build graph for k = 47
2022-04-08 01:10:18 - Assemble contigs from SdBG for k = 47
2022-04-08 01:10:20 - Local assembly for k = 47
2022-04-08 01:10:39 - Extract iterative edges from k = 47 to 63
2022-04-08 01:10:41 - Build graph for k = 63
2022-04-08 01:10:42 - Assemble contigs from SdBG for k = 63
2022-04-08 01:10:44 - Local assembly for k = 63
2022-04-08 01:11:03 - Extract iterative edges from k = 63 to 79
2022-04-08 01:11:05 - Build graph for k = 79
2022-04-08 01:11:06 - Assemble contigs from SdBG for k = 79
2022-04-08 01:11:08 - Local assembly for k = 79
2022-04-08 01:11:28 - Extract iterative edges from k = 79 to 95
2022-04-08 01:11:30 - Build graph for k = 95
2022-04-08 01:11:31 - Assemble contigs from SdBG for k = 95
2022-04-08 01:11:33 - Local assembly for k = 95
2022-04-08 01:11:49 - Extract iterative edges from k = 95 to 111
2022-04-08 01:11:50 - Build graph for k = 111
2022-04-08 01:11:51 - Assemble contigs from SdBG for k = 111
2022-04-08 01:11:53 - Local assembly for k = 111
2022-04-08 01:12:08 - Extract iterative edges from k = 111 to 127
2022-04-08 01:12:09 - Build graph for k = 127
2022-04-08 01:12:10 - Assemble contigs from SdBG for k = 127
2022-04-08 01:12:12 - Local assembly for k = 127
2022-04-08 01:12:26 - Extract iterative edges from k = 127 to 143
2022-04-08 01:12:26 - Build graph for k = 143
2022-04-08 01:12:27 - Assemble contigs from SdBG for k = 143
2022-04-08 01:12:29 - Local assembly for k = 143
2022-04-08 01:12:40 - Extract iterative edges from k = 143 to 159
2022-04-08 01:12:40 - Build graph for k = 159
2022-04-08 01:12:41 - Assemble contigs from SdBG for k = 159
2022-04-08 01:12:43 - Local assembly for k = 159
2022-04-08 01:12:53 - Extract iterative edges from k = 159 to 175
2022-04-08 01:12:54 - Build graph for k = 175
2022-04-08 01:12:54 - Assemble contigs from SdBG for k = 175
2022-04-08 01:12:56 - Merging to output final contigs
2022-04-08 01:12:56 - 1850 contigs, total 2031858 bp, min 182 bp, max 26295 bp, avg 1098 bp, N50 1616 bp
2022-04-08 01:12:56 - ALL DONE. Time elapsed: 206.394586 seconds
9. captus-assembly_assemble.stats.tsv
Statistics tab-separated-values table compiled across all assembled samples.
Column
Description
sample
Name of the sample
n_contigs
Number of contigs
pct_contigs_>=_1kbp
Percentage of contigs over 1kbp
pct_contigs_>=_2kbp
Percentage of contigs over 2kbp
pct_contigs_>=_5kbp
Percentage of contigs over 5kbp
pct_contigs_>=_10kbp
Percentage of contigs over 10kbp
longest_contig
Length of longest contig in bp
shortest_contig
Length of shortest contig in bp
total_length
Cumulative length of all contigs in bp
pct_length_>=_1kbp
Percentage of total assembly length in contigs over 1kbp
pct_length_>=_2kbp
Percentage of total assembly length in contigs over 2kbp
pct_length_>=_5kbp
Percentage of total assembly length in contigs over 5kbp
pct_length_>=_10kbp
Percentage of total assembly length in contigs over 10kbp
avg_length
Average contig length in bp
median_length
Median contig length in bp
N50
Assembly N50 in bp
GC_content
Average contig GC content
avg_depth
Average contig depth
pct_contigs_>=_1x
Percentage of contigs over 1x depth
pct_contigs_>=_2x
Percentage of contigs over 2x depth
pct_contigs_>=_5x
Percentage of contigs over 5x depth
pct_contigs_>=_10x
Percentage of contigs over 10x depth
filtered_n_contigs
filtered_total_length
filtered_avg_length
filtered_gc_content
10. captus-assembly_assemble.report.html
This is the final Assembly report, summarizing statistics across all samples assembled.
11. captus-assembly_assemble.log
This is the log from Captus, it contains the command used and all the information shown during the run. If the option --show_less was enabled, the log will also contain all the extra detailed information that was hidden during the run.
